3PAJ | pdb_00003paj

2.00 Angstrom resolution crystal structure of a quinolinate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3PAJ/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-10-19 Released: 2010-11-03
Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., Peterson, S., 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:
0.222 (Depositor), 0.234 (DCC)
R-Value Work:
0.173 (Depositor), 0.185 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

2.00 Angstrom resolution crystal structure of a quinolinate phosphoribosyltransferase from Vibrio cholerae O1 biovar eltor str. N16961

Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 69.69 kDa
Atom Count: 5,158
Modeled Residue Count: 599
Deposited Residue Count: 640
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide pyrophosphorylase, carboxylating	A, B	320	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_2422 EC: 2.4.2.19
UniProt
Find proteins for Q9KPE6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPE6 Go to UniProtKB: Q9KPE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KPE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.222 (Depositor), 0.234 (DCC)
R-Value Work: 0.173 (Depositor), 0.185 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.195	α = 90
b = 79.551	β = 90
c = 117.908	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-11-03
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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.