3SGW

Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1186/1472-6807-11-39
  • Primary Citation of Related Structures:  

  • 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 p ...

    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.


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. tedwards@embios.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ribose 5-phosphate isomerase
A
184Coccidioides immitis (strain RS)Mutation(s): 0 
EC: 5.3.1.-
Find proteins for P0CL19 (Coccidioides immitis (strain RS))
Go to UniProtKB:  P0CL19
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 77.460α = 90.00
b = 84.420β = 90.00
c = 96.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
StructureStudiodata collection
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-26
    Type: Database references
  • Version 1.3: 2015-04-29
    Type: Non-polymer description