3GNN | pdb_00003gnn

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei

PDB DOI: https://doi.org/10.2210/pdb3GNN/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia pseudomallei 1710b, unidentified
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-17 Released: 2009-03-31
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.273 (Depositor), 0.269 (DCC)
R-Value Work:
0.214 (Depositor), 0.213 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 64.55 kDa
Atom Count: 3,879
Modeled Residue Count: 518
Deposited Residue Count: 604
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nicotinate-nucleotide diphosphorylase (carboxylating)	A, B	298	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: nadC, BURPS1710b_1132 EC: 2.4.2.19
UniProt
Find proteins for Q3JV59 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JV59 Go to UniProtKB: Q3JV59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3JV59
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown Peptide	C [auth D], D [auth E]	4	unidentified	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.273 (Depositor), 0.269 (DCC)
R-Value Work: 0.214 (Depositor), 0.213 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.978	α = 90
b = 57.414	β = 106.74
c = 66.243	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary

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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.