3OOW | pdb_00003oow

Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from Francisella tularensis subsp. tularensis SCHU S4.

PDB DOI: https://doi.org/10.2210/pdb3OOW/pdb

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

Deposited: 2010-08-31 Released: 2010-09-15
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, F.W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from Francisella tularensis subsp. tularensis SCHU S4.

Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, F.W.

To be published.

Macromolecule Content

Total Structure Weight: 145.7 kDa
Atom Count: 10,270
Modelled Residue Count: 1,287
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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(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	166	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
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain PA [auth F] SDF format, chain UA [auth G] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain PA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain PA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain X [auth C]	DA [auth D], PA [auth F], UA [auth G], X [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain DA [auth D] Focus chain PA [auth F] Focus chain UA [auth G] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain PA [auth F] Focus chain UA [auth G] Focus chain X [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain BB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AB [auth H] BB [auth H] EA [auth D] FA [auth D] JA [auth E] AB [auth H], BB [auth H], EA [auth D], FA [auth D], JA [auth E], K [auth A], KA [auth E], L [auth A], M [auth A], Q [auth B], QA [auth F], R [auth B], RA [auth F], VA [auth G], WA [auth G], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain Y [auth C] Focus chain Z [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CB [auth H] SDF format, chain DB [auth H] SDF format, chain GA [auth D] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain XA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain DB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain DB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain XA [auth G]	AA [auth C] CB [auth H] DB [auth H] GA [auth D] LA [auth E] AA [auth C], CB [auth H], DB [auth H], GA [auth D], LA [auth E], MA [auth E], N [auth A], O [auth A], S [auth B], SA [auth F], T [auth B], U [auth B], XA [auth G]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CB [auth H] Focus chain DB [auth H] Focus chain GA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain XA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain CB [auth H] Focus chain DB [auth H] Focus chain GA [auth D] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain XA [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain TA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H]	BA [auth D] CA [auth D] HA [auth E] I [auth A] IA [auth E] BA [auth D], CA [auth D], HA [auth E], I [auth A], IA [auth E], J [auth A], NA [auth F], OA [auth F], P [auth B], TA [auth G], V [auth C], W [auth C], YA [auth H], ZA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain TA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain TA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain YA [auth H] Focus chain ZA [auth H]

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: 1.75 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.168 (Depositor), 0.180 (DCC)
R-Value Observed: 0.170 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33oow

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.56	α = 90
b = 96.3	β = 90
c = 128.62	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

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-09-15
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: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-10-09
Changes: Structure summary