4EM8 | pdb_00004em8

The Structure of Ribose 5-phosphate Isomerase B from Anaplasma phagocytophilum

• PDB DOI: https://doi.org/10.2210/pdb4EM8/pdb

• Classification: ISOMERASE
• Organism(s): Anaplasma phagocytophilum str. HZ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-11 Released: 2012-04-25 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The Structure of Ribose 5-phosphate Isomerase B from Anaplasma phagocytophilum

Clifton, M.C., Edwards, T.E., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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)

Macromolecule Content 

• Total Structure Weight: 32.39 kDa 
• Atom Count: 2,347 
• Modeled Residue Count: 291 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase B	A, B	148	Anaplasma phagocytophilum str. HZ	Mutation(s): 0  Gene Names: rpiB, APH_0642 EC: 5.3.1.6
UniProt
Find proteins for Q2GK74 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GK74  Go to UniProtKB:  Q2GK74

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.36	α = 90
b = 62.49	β = 93.13
c = 73.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description