3HHE | pdb_00003hhe

Crystal structure of ribose-5-phosphate isomerase A from Bartonella henselae

• PDB DOI: https://doi.org/10.2210/pdb3HHE/pdb

• Classification: ISOMERASE
• Organism(s): Bartonella henselae str. Houston-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-15 Released: 2009-05-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ribose-5-phosphate isomerase A from Bartonella henselae

Edwards, T.E., Abendroth, J.A., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.53 kDa 
• Atom Count: 3,654 
• Modeled Residue Count: 466 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B	255	Bartonella henselae str. Houston-1	Mutation(s): 0  Gene Names: rpiA, BH06410 EC: 5.3.1.6
UniProt
Find proteins for Q6G3V6 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / CCUG 30454 / Houston 1)) Explore Q6G3V6  Go to UniProtKB:  Q6G3V6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP	C [auth A], F [auth B]	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N
K	D [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.19	α = 90
b = 79.584	β = 90
c = 151.127	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description