3ONO

Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3ONO/pdb

• Classification: ISOMERASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-08-30 Released: 2010-09-08 
• Deposition Author(s): Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus

Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A.

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: 23.24 kDa 
• Atom Count: 1,915 
• Modelled Residue Count: 212 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose/Galactose Isomerase	A	214	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VPA0080
UniProt
Find proteins for Q87K18 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87K18  Go to UniProtKB:  Q87K18

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.924	α = 90
b = 62.924	β = 90
c = 242.3	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Kim, Y., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance