3OFV | pdb_00003ofv

Crystal structure of peptidyl-tRNA hydrolase from Escherichia Coli, I222 crystal form

• PDB DOI: https://doi.org/10.2210/pdb3OFV/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli B354
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-16 Released: 2011-08-17 
• Deposition Author(s): Lam, R., McGrath, T.E., Romanov, V., Gothe, S.A., Peddi, S.R., Razumova, E., Lipman, R.S., Branstrom, A.A., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of peptidyl-tRNA hydrolase from Escherichia Coli, I222 crystal form

Lam, R., McGrath, T.E., Romanov, V., Gothe, S.A., Peddi, S.R., Razumova, E., Lipman, R.S., Branstrom, A.A., Chirgadze, N.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.77 kDa 
• Atom Count: 4,335 
• Modeled Residue Count: 581 
• Deposited Residue Count: 633 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B, C	211	Escherichia coli B354	Mutation(s): 0  Gene Names: ECEG_00530, ECs1709, pth EC: 3.1.1.29

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.38	α = 90
b = 96.96	β = 90
c = 207.678	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Lam, R., McGrath, T.E., Romanov, V., Gothe, S.A., Peddi, S.R., Razumova, E., Lipman, R.S., Branstrom, A.A., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description