3OPQ

Phosphoribosylaminoimidazole carboxylase with fructose-6-phosphate bound to the central channel of the octameric protein structure.

PDB DOI: https://doi.org/10.2210/pdb3OPQ/pdb

Classification: LYASE
Organism(s): Francisella tularensis subsp. tularensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-01 Released: 2010-11-17
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.242 (DCC)
R-Value Work:
0.188 (Depositor), 0.196 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Phosphoribosylaminoimidazole carboxylase with fructose-6-phosphate bound to the central channel of the octameric protein structure.

Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 142.67 kDa
Atom Count: 10,071
Modelled Residue Count: 1,282
Deposited Residue Count: 1,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase,catalytic subunit	A, B, C, D, E A, B, C, D, E, F, G, H	163	Francisella tularensis subsp. tularensis	Mutation(s): 0 Gene Names: FTT_0896, purE EC: 4.1.1.21 (PDB Primary Data), 5.4.99.18 (UniProt)
UniProt
Find proteins for Q5NGE9 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NGE9 Go to UniProtKB: Q5NGE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NGE9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F6R Query on F6R Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain U [auth D] MOL2 format, chain IA [auth G] MOL2 format, chain U [auth D] mmCIF format, chain IA [auth G] mmCIF format, chain U [auth D]	IA [auth G], U [auth D]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain IA [auth G] Focus chain U [auth D] Interactions & Density Focus chain IA [auth G] Focus chain U [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain I [auth A] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain Z [auth E] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain V [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth E] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth E] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain V [auth D]	CA [auth F] FA [auth G] I [auth A] J [auth A] JA [auth H] CA [auth F], FA [auth G], I [auth A], J [auth A], JA [auth H], KA [auth H], M [auth B], N [auth B], R [auth C], V [auth D], Z [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain GA [auth G] SDF format, chain LA [auth H] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain GA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] GA [auth G] AA [auth E], BA [auth E], DA [auth F], EA [auth F], GA [auth G], HA [auth G], K [auth A], LA [auth H], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.242 (DCC)
R-Value Work: 0.188 (Depositor), 0.196 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33opq

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.59	α = 90
b = 96.67	β = 90
c = 128.48	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CCP4	model building
MrBUMP	phasing
PHENIX	model building
REFMAC	refinement
XSCALE	data scaling
CCP4	phasing
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary