2CMU | pdb_00002cmu

Crystal structure of a putative peptidyl-arginine deiminase

• PDB DOI: https://doi.org/10.2210/pdb2CMU/pdb
• Entry: 2CMU supersedes: 1X72

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2006-05-13 Released: 2006-05-24 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Solorzano, V., Lima, C.D., New York Structural GenomiX Research Consortium (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal Structure of a Putative Peptidyl-Arginine Deiminase.

R Rajashankar, K., Kniewel, R., Solorzano, V., Lima, C.D.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 39.35 kDa 
• Atom Count: 2,832 
• Modelled Residue Count: 335 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE PEPTIDYL-ARGININE DEIMINASE	A	342	Helicobacter pylori 26695	Mutation(s): 0  EC: 3.5.3.6
UniProt
Find proteins for O24890 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24890  Go to UniProtKB:  O24890

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.049	α = 90
b = 52.049	β = 90
c = 248.022	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-24 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Solorzano, V., Lima, C.D., New York Structural GenomiX Research Consortium (NYSGXRC)
• This entry supersedes: 1X72

Revision History  

• Version 1.0: 2006-05-24
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2015-09-02
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-08-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-11-13
  Changes: Data collection, Database references, Other, Structure summary