6W6A | pdb_00006w6a

Crystal structure of a pyridoxine 5'-phosphate synthease from Stenotrophomonas maltophilia K279a

PDB DOI: https://doi.org/10.2210/pdb6W6A/pdb

Classification: LYASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-16 Released: 2020-03-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.234 (Depositor), 0.235 (DCC)
R-Value Work:
0.195 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a pyridoxine 5'-phosphate synthease from Stenotrophomonas maltophilia K279a

Edwards, T.E., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 54.71 kDa
Atom Count: 3,754
Modeled Residue Count: 495
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine 5'-phosphate synthase	A, B	255	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: pdxJ, Smlt0015 EC: 2.6.99.2
UniProt
Find proteins for B2FT93 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FT93 Go to UniProtKB: B2FT93
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2FT93
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.234 (Depositor), 0.235 (DCC)
R-Value Work: 0.195 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.78	α = 90
b = 57.47	β = 102.4
c = 71.77	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-03-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-03-25
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.