3DB0

Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DB0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Listeria innocua
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-30 Released: 2008-07-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239
R-Value Work: 0.182
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 29.21 kDa
Atom Count: 1,995
Modelled Residue Count: 240
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin2891 protein	A, B	128	Listeria innocua	Mutation(s): 0 Gene Names: lin2891
UniProt
Find proteins for Q926Z8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q926Z8 Go to UniProtKB: Q926Z8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q926Z8
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.00 Å
R-Value Free: 0.239
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M33DB0

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.16	α = 90
b = 42.23	β = 91.59
c = 62.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.