3TJ4 | pdb_00003tj4

Crystal structure of an enolase from agrobacterium tumefaciens (efi target efi-502087) no mg

PDB DOI: https://doi.org/10.2210/pdb3TJ4/pdb

Classification: LYASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-23 Released: 2011-09-14
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Wasserman, S.R., Morisco, L.L., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.165 (Depositor), 0.160 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an enolase from agrobacterium tumefaciens (efi target efi-502087) no mg

Vetting, M.W., Bouvier, J.T., Wasserman, S.R., Morisco, L.L., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 83.63 kDa
Atom Count: 6,811
Modelled Residue Count: 720
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase	A, B	372	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: AGR_L_1470, Atu4120
UniProt
Find proteins for Q7CU39 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CU39 Go to UniProtKB: Q7CU39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7CU39
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	H [auth A] I [auth A] J [auth A] N [auth B] O [auth B] H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B]	K [auth A], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.165 (Depositor), 0.160 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.739	α = 90
b = 118.739	β = 90
c = 113.423	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-14

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-09-14
Type: Initial release
Version 1.1: 2011-10-12
Changes: Structure summary
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description