3SDW

Crystal structure of a ribose-5-phosphate isomerase B RpiB from Coccidioides immitis bound to phosphate

• PDB DOI: https://doi.org/10.2210/pdb3SDW/pdb

• Classification: ISOMERASE
• Organism(s): Coccidioides immitis RS
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-09 Released: 2011-06-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.176 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis.

Edwards, T.E., Abramov, A.B., Smith, E.R., Baydo, R.O., Leonard, J.T., Leibly, D.J., Thompkins, K.B., Clifton, M.C., Gardberg, A.S., Staker, B.L., Van Voorhis, W.C., Myler, P.J., Stewart, L.J.

(2011) BMC Struct Biol 11: 39-39

• PubMed: 21995815 
• DOI: https://doi.org/10.1186/1472-6807-11-39
• Primary Citation of Related Structures:  
  3QD5, 3SDW, 3SGW


• PubMed Abstract: 
  

  Ribose-5-phosphate isomerase is an enzyme that catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate. This family of enzymes naturally occurs in two distinct classes, RpiA and RpiB, which play an important role in the pentose phosphate pathway and nucleotide and co-factor biogenesis.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. [e-mail]

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 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.96 kDa 
• Atom Count: 1,385 
• Modelled Residue Count: 158 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribose 5-phosphate isomerase	A	184	Coccidioides immitis RS	Mutation(s): 0  Gene Names: CIMG_07932 EC: 5.3.1
UniProt
Find proteins for P0CL19 (Coccidioides immitis (strain RS)) Explore P0CL19  Go to UniProtKB:  P0CL19

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.176 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: F 2 2 2
• Diffraction Data: https://doi.org/10.18430/M33SDW

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.7	α = 90
b = 85.22	β = 90
c = 96.29	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-10-26
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description