3BA3 | pdb_00003ba3

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BA3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactiplantibacillus plantarum WCFS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-07 Released: 2007-11-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.196 (Depositor), 0.200 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 33.23 kDa
Atom Count: 2,828
Modeled Residue Count: 287
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase-like protein	A, B	145	Lactiplantibacillus plantarum WCFS1	Mutation(s): 0 Gene Names: NP_783940.1, lp_0091
UniProt
Find proteins for F9USS0 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9USS0 Go to UniProtKB: F9USS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F9USS0
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] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain H [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 A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [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: 1.55 Å
R-Value Free: 0.196 (Depositor), 0.200 (DCC)
R-Value Work: 0.170 (Depositor), 0.180 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BA3

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.379	α = 90
b = 137.379	β = 90
c = 137.379	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-09
Changes: Data collection, Structure summary

Prepare Data

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Deposit Data

Help and Resources

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Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3BA3 | pdb_00003ba3