5JLA

Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M

• PDB DOI: https://doi.org/10.2210/pdb5JLA/pdb

• Classification: ISOMERASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-26 Released: 2016-05-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of putative short-chain dehdrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD

SSGCID, Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 115.93 kDa 
• Atom Count: 8,601 
• Modelled Residue Count: 1,032 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short-chain dehydrogenase/reductase	A, B, C, D	274	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxe_C0850
UniProt
Find proteins for Q13GR0 (Paraburkholderia xenovorans (strain LB400)) Explore Q13GR0  Go to UniProtKB:  Q13GR0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.48	α = 90
b = 109.96	β = 93.9
c = 64.99	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description