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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (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

Entry History 

Deposition Data

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

Revision History  

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