2QL3 | pdb_00002ql3

Crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1

PDB DOI: https://doi.org/10.2210/pdb2QL3/pdb

Classification: TRANSCRIPTION
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-07-12 Released: 2007-07-24
Deposition Author(s): Tan, K., Skarina, T., Kagen, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1.

Tan, K., Skarina, T., Kagen, O., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 282.47 kDa
Atom Count: 20,701
Modelled Residue Count: 2,460
Deposited Residue Count: 2,508
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulator, LysR family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	209	Rhodococcus jostii RHA1	Mutation(s): 5 Gene Names: RHA1_ro01847
UniProt
Find proteins for Q0SFM8 (Rhodococcus jostii (strain RHA1)) Explore Q0SFM8 Go to UniProtKB: Q0SFM8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SFM8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain BC [auth K] SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain DC [auth K] SDF format, chain EC [auth L] SDF format, chain FA [auth D] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GC [auth L] SDF format, chain HA [auth D] SDF format, chain IA [auth E] SDF format, chain IC [auth L] SDF format, chain JA [auth E] SDF format, chain JC [auth L] SDF format, chain KA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain MB [auth I] SDF format, chain N [auth A] SDF format, chain NB [auth J] SDF format, chain OB [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain QB [auth J] SDF format, chain R [auth A] SDF format, chain RA [auth F] SDF format, chain RB [auth J] SDF format, chain SA [auth F] SDF format, chain SB [auth J] SDF format, chain T [auth B] SDF format, chain TB [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth F] SDF format, chain UB [auth K] SDF format, chain VA [auth F] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain YB [auth K] SDF format, chain Z [auth C] SDF format, chain ZB [auth K] SDF format, chain AA [auth C] SDF format, chain AB [auth G] SDF format, chain AC [auth K] SDF format, chain CA [auth C] SDF format, chain CC [auth K] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FC [auth L] SDF format, chain GB [auth I] SDF format, chain HB [auth I] SDF format, chain HC [auth L] SDF format, chain IB [auth I] SDF format, chain JB [auth I] SDF format, chain KB [auth I] SDF format, chain LA [auth F] SDF format, chain LB [auth I] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain PB [auth J] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain TA [auth F] SDF format, chain V [auth B] SDF format, chain VB [auth K] SDF format, chain WB [auth K] SDF format, chain X [auth C] SDF format, chain XB [auth K] SDF format, chain ZA [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain BC [auth K] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain DC [auth K] MOL2 format, chain EC [auth L] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GC [auth L] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain IC [auth L] MOL2 format, chain JA [auth E] MOL2 format, chain JC [auth L] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain MB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth J] MOL2 format, chain OB [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth J] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth J] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth K] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain YB [auth K] MOL2 format, chain Z [auth C] MOL2 format, chain ZB [auth K] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth K] MOL2 format, chain CA [auth C] MOL2 format, chain CC [auth K] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FC [auth L] MOL2 format, chain GB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain HC [auth L] MOL2 format, chain IB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth I] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PB [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain WB [auth K] MOL2 format, chain X [auth C] MOL2 format, chain XB [auth K] MOL2 format, chain ZA [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth G] mmCIF format, chain BC [auth K] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain DC [auth K] mmCIF format, chain EC [auth L] mmCIF format, chain FA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GC [auth L] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain IC [auth L] mmCIF format, chain JA [auth E] mmCIF format, chain JC [auth L] mmCIF format, chain KA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain MB [auth I] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth J] mmCIF format, chain OB [auth J] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain QB [auth J] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain RB [auth J] mmCIF format, chain SA [auth F] mmCIF format, chain SB [auth J] mmCIF format, chain T [auth B] mmCIF format, chain TB [auth J] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain UB [auth K] mmCIF format, chain VA [auth F] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain YB [auth K] mmCIF format, chain Z [auth C] mmCIF format, chain ZB [auth K] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain AC [auth K] mmCIF format, chain CA [auth C] mmCIF format, chain CC [auth K] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain FC [auth L] mmCIF format, chain GB [auth I] mmCIF format, chain HB [auth I] mmCIF format, chain HC [auth L] mmCIF format, chain IB [auth I] mmCIF format, chain JB [auth I] mmCIF format, chain KB [auth I] mmCIF format, chain LA [auth F] mmCIF format, chain LB [auth I] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain PB [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain VB [auth K] mmCIF format, chain WB [auth K] mmCIF format, chain X [auth C] mmCIF format, chain XB [auth K] mmCIF format, chain ZA [auth G]	AA [auth C] AB [auth G] AC [auth K] BA [auth C] BB [auth G] AA [auth C], AB [auth G], AC [auth K], BA [auth C], BB [auth G], BC [auth K], CA [auth C], CB [auth H], CC [auth K], DA [auth D], DB [auth H], DC [auth K], EA [auth D], EB [auth H], EC [auth L], FA [auth D], FB [auth H], FC [auth L], GA [auth D], GB [auth I], GC [auth L], HA [auth D], HB [auth I], HC [auth L], IA [auth E], IB [auth I], IC [auth L], JA [auth E], JB [auth I], JC [auth L], KA [auth E], KB [auth I], LA [auth F], LB [auth I], M [auth A], MA [auth F], MB [auth I], N [auth A], NA [auth F], NB [auth J], O [auth A], OA [auth F], OB [auth J], P [auth A], PA [auth F], PB [auth J], Q [auth A], QA [auth F], QB [auth J], R [auth A], RA [auth F], RB [auth J], S [auth B], SA [auth F], SB [auth J], T [auth B], TA [auth F], TB [auth J], U [auth B], UA [auth F], UB [auth K], V [auth B], VA [auth F], VB [auth K], W [auth B], WA [auth F], WB [auth K], X [auth C], XA [auth F], XB [auth K], Y [auth C], YA [auth F], YB [auth K], Z [auth C], ZA [auth G], ZB [auth K]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain AC [auth K] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain BC [auth K] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain CC [auth K] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain DC [auth K] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain EC [auth L] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain FC [auth L] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain GC [auth L] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain HC [auth L] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain IC [auth L] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain JC [auth L] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth F] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth J] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth A] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain T [auth B] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth C] Focus chain XA [auth F] Focus chain XB [auth K] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain YB [auth K] Focus chain Z [auth C] Focus chain ZA [auth G] Focus chain ZB [auth K] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain AC [auth K] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain BC [auth K] Focus chain CA [auth C] Focus chain CB [auth H] Focus chain CC [auth K] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain DC [auth K] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain EC [auth L] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain FC [auth L] Focus chain GA [auth D] Focus chain GB [auth I] Focus chain GC [auth L] Focus chain HA [auth D] Focus chain HB [auth I] Focus chain HC [auth L] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain IC [auth L] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain JC [auth L] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth F] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain NB [auth J] Focus chain O [auth A] Focus chain OA [auth F] Focus chain OB [auth J] Focus chain P [auth A] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth A] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth A] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain S [auth B] Focus chain SA [auth F] Focus chain SB [auth J] Focus chain T [auth B] Focus chain TA [auth F] Focus chain TB [auth J] Focus chain U [auth B] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain VB [auth K] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth K] Focus chain X [auth C] Focus chain XA [auth F] Focus chain XB [auth K] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain YB [auth K] Focus chain Z [auth C] Focus chain ZA [auth G] Focus chain ZB [auth K]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.277	α = 90
b = 114.277	β = 90
c = 175.359	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary