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.

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
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This is version 1.2 of the entry. See complete history.

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.

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

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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
UniProt
Find proteins for P0A7D1 (Escherichia coli (strain K12)) Explore P0A7D1 Go to UniProtKB: P0A7D1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7D1
Sequence Annotations Expand
Reference Sequence

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

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Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Branstrom, A.A.

Chirgadze, N.Y.

Revision History (Full details and data files)

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