2P1Z | pdb_00002p1z

Crystal structure of phosphoribosyltransferase from Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb2P1Z/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium diphtheriae NCTC 13129
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-06 Released: 2007-04-03 
• Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystal structure of phosphoribosyltransferase from Corynebacterium diphtheriae

Chang, C., Li, H., Clancy, S., Joachimiak, A.

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: 38.6 kDa 
• Atom Count: 2,513 
• Modeled Residue Count: 326 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosyltransferase	A, B	180	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 3  Gene Names: pyrE, DIP2097 EC: 2.4.2.10
UniProt
Find proteins for Q8NM11 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NM11  Go to UniProtKB:  Q8NM11

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: 2.44 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.438	α = 90
b = 103.709	β = 90
c = 39.417	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Chang, C., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary