6W4U | pdb_00006w4u

Crystal structure of Triosephosphate isomerase from Stenotrophomonas maltophilia K279a

• PDB DOI: https://doi.org/10.2210/pdb6W4U/pdb

• Classification: ISOMERASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-03-11 Released: 2020-04-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Triosephosphate isomerase from Stenotrophomonas maltophilia K279a

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

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: 54.61 kDa 
• Atom Count: 4,081 
• Modeled Residue Count: 505 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	259	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: tpiA, Smlt3407 EC: 5.3.1.1
UniProt
Find proteins for B2FNY1 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FNY1  Go to UniProtKB:  B2FNY1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36w4u

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.5	α = 71.9
b = 46.66	β = 71.086
c = 66.83	γ = 68.356

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Derived calculations, Refinement description