4LA4 | pdb_00004la4

Crystal structure of native PnpB

PDB DOI: https://doi.org/10.2210/pdb4LA4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas sp. WBC-3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-19 Released: 2014-06-25
Deposition Author(s): Su, J., Zhang, C., Li, N., Gu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.210 (Depositor), 0.200 (DCC)
R-Value Work:
0.176 (Depositor), 0.170 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of native PnpB

Su, J., Zhang, C., Li, N., Gu, L.

To be published.

Macromolecule Content

Total Structure Weight: 44.12 kDa
Atom Count: 3,042
Modeled Residue Count: 393
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase (quinone)	A, B	207	Pseudomonas sp. WBC-3	Mutation(s): 0 Gene Names: pnpB EC: 1.6.5.2 (PDB Primary Data), 1.6.5.6 (UniProt)
UniProt
Find proteins for C1I202 (Pseudomonas sp. (strain WBC-3)) Explore C1I202 Go to UniProtKB: C1I202
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C1I202
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.210 (Depositor), 0.200 (DCC)
R-Value Work: 0.176 (Depositor), 0.170 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.145	α = 90
b = 73.11	β = 90
c = 84.965	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-06-25
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

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.