3M84 | pdb_00003m84

Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis

PDB DOI: https://doi.org/10.2210/pdb3M84/pdb

Classification: LIGASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-17 Released: 2010-07-14
Deposition Author(s): Maltseva, N., Kim, Y., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.183 (Depositor), 0.179 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis

Maltseva, N., Kim, Y., Hasseman, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 79.58 kDa
Atom Count: 6,757
Modeled Residue Count: 698
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylformylglycinamidine cyclo-ligase	A, B	350	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: purM EC: 6.3.3.1
UniProt
Find proteins for Q5NGF2 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NGF2 Go to UniProtKB: Q5NGF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NGF2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain V [auth B] MOL2 format, chain V [auth B] mmCIF format, chain V [auth B]	V [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain V [auth B] Interactions & Density Focus chain V [auth B]
SO4 Query on SO4 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 G [auth A] SDF format, chain K [auth A] SDF format, chain L [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] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [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] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [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] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B]	C [auth A] D [auth A] E [auth A] G [auth A] K [auth A] C [auth A], D [auth A], E [auth A], G [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	H [auth A], J [auth A], U [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain U [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.183 (Depositor), 0.179 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.155 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33m84

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.708	α = 90
b = 90.56	β = 90
c = 118.989	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELX	model building
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-07-14
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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary