2HTD

CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2HTD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-07-25 Released: 2006-08-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.206
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase (ZP_00387536.1) from Lactobacillus delbrueckii bulgaricus ATCC BAA-365 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 32.21 kDa
Atom Count: 2,156
Modelled Residue Count: 246
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase	A, B	140	Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365	Mutation(s): 0 Gene Names: ZP_00387536.1
UniProt
Find proteins for Q1GBW8 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)) Explore Q1GBW8 Go to UniProtKB: Q1GBW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1GBW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

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: 1.60 Å
R-Value Free: 0.206
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M32HTD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.104	α = 90
b = 71.123	β = 90.86
c = 47.031	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-08-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-08-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, Refinement description

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Help and Resources

2HTD

CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION

Crystal structure of Predicted flavin-nucleotide-binding protein from COG3576 family structurally related to pyridoxine 5'-phosphate oxidase (ZP_00387536.1) from Lactobacillus delbrueckii bulgaricus ATCC BAA-365 at 1.60 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)