3OS4 | pdb_00003os4

The Crystal Structure of Nicotinate Phosphoribosyltransferase from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3OS4/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-08 Released: 2010-09-22
Deposition Author(s): Maltseva, N., Kim, Y., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.193 (Depositor), 0.191 (DCC)
R-Value Work:
0.162 (Depositor), 0.159 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of Nicotinate Phosphoribosyltransferase from Yersinia pestis

Maltseva, N., Kim, Y., Gu, M., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 95.61 kDa
Atom Count: 7,855
Modeled Residue Count: 758
Deposited Residue Count: 814
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate phosphoribosyltransferase	A, B	407	Yersinia pestis CO92	Mutation(s): 0 Gene Names: pncB, y2757, YPO1413, YP_1180 EC: 2.4.2.11 (PDB Primary Data), 6.3.4.21 (UniProt)
UniProt
Find proteins for Q8ZG93 (Yersinia pestis) Explore Q8ZG93 Go to UniProtKB: Q8ZG93
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZG93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B]	E [auth A], M [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth B]	D [auth A], I [auth A], O [auth B], P [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B]	F [auth A], L [auth A], R [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth A] Focus chain R [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B]	H [auth A], J [auth A], K [auth A], Q [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain T [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain U [auth B]	C [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain U [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: 1.60 Å
R-Value Free: 0.193 (Depositor), 0.191 (DCC)
R-Value Work: 0.162 (Depositor), 0.159 (DCC)
R-Value Observed: 0.163 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.394	α = 81.95
b = 50.681	β = 83.39
c = 87.184	γ = 71.95

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-09-22
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: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary