1LKZ | pdb_00001lkz

Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli.

• PDB DOI: https://doi.org/10.2210/pdb1LKZ/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-04-26 Released: 2002-05-08 
• Deposition Author(s): Rangarajan, E.S., Sivaraman, J., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.235 (DCC) 

Literature

Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli

Rangarajan, E.S., Sivaraman, J., Matte, A., Cygler, M.

(2002) Proteins 48: 737-740

• PubMed: 12211039 
• DOI: https://doi.org/10.1002/prot.10203
• Primary Citation of Related Structures:  
  1LKZ

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Organizational Affiliation: 

Department of Biochemistry, McGill University, Montreal, Quebec, Canada.

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: 46.42 kDa 
• Atom Count: 3,335 
• Modelled Residue Count: 438 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase A	A, B	219	Escherichia coli	Mutation(s): 7  EC: 5.3.1.6
UniProt
Find proteins for P0A7Z0 (Escherichia coli (strain K12)) Explore P0A7Z0  Go to UniProtKB:  P0A7Z0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.235 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.335	α = 90
b = 71.809	β = 90
c = 193.067	γ = 90

Software Package:

Software Name	Purpose
Adxv	data processing
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-08 
Deposition Author(s): Rangarajan, E.S., Sivaraman, J., Matte, A., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

Revision History  

• Version 1.0: 2002-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary