2CX5

Crystal structure of a putative trans-editing enzyme for prolyl tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb2CX5/pdb

Classification: TRANSLATION
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-06-28 Released: 2005-12-28
Deposition Author(s): Murayama, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245
R-Value Work: 0.197
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative trans-editing enzyme for prolyl tRNA synthetase

Murayama, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 66.3 kDa
Atom Count: 5,167
Modelled Residue Count: 628
Deposited Residue Count: 632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A PUTATIVE TRANS-EDITING ENZYME	A, B, C, D	158	Thermus thermophilus	Mutation(s): 0
UniProt
Find proteins for Q5SHN1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN1 Go to UniProtKB: Q5SHN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SHN1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245
R-Value Work: 0.197
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.576	α = 90
b = 61.245	β = 110.77
c = 84.186	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-12-28

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-12-28
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.