Macromolecule Content

Total Structure Weight: 29208.21
Atom Count: 1886
Residue Count: 256
Unique protein chains: 1

3DB0

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

DOI: 10.2210/pdb3DB0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
Expression System: Escherichia coli

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 Å
R-Value Free: 0.239
R-Value Work: 0.182

wwPDB Validation3D Report Full Report

This is version 1.2 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.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lin2891 protein	A, B	128	Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)	Mutation(s): 0
Find proteins for Q926Z8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Go to UniProtKB: Q926Z8
Protein Feature View Full Protein Feature View for Q926Z8

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 Å
R-Value Free: 0.239
R-Value Work: 0.182
Space Group: C 1 2 1
Diffraction Data DOI:
10.18430/M33DB0 Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 92.160	α = 90.00
b = 42.230	β = 91.59
c = 62.020	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

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

Revision History

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Type: Advisory, Version format compliance
Version 1.2: 2017-10-25
Type: Author supporting evidence, Refinement description

The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.