2DBO | pdb_00002dbo

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb2DBO/pdb

Classification: HYDROLASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-12-15 Released: 2006-06-15
Deposition Author(s): Ishii, T., Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.284 (Depositor), 0.280 (DCC)
R-Value Work:
0.230 (Depositor), 0.229 (DCC)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Aquifex aeolicus

Ishii, T., Shibata, R., Bessho, Y., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 16.99 kDa
Atom Count: 1,228
Modeled Residue Count: 148
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-tyrosyl-tRNA(Tyr) deacylase	A	148	Aquifex aeolicus VF5	Mutation(s): 0 EC: 3.1 (PDB Primary Data), 3.1.1.96 (UniProt)
UniProt
Find proteins for O66742 (Aquifex aeolicus (strain VF5)) Explore O66742 Go to UniProtKB: O66742
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66742
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.284 (Depositor), 0.280 (DCC)
R-Value Work: 0.230 (Depositor), 0.229 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.01	α = 90
b = 76.01	β = 90
c = 133.754	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-06-15

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-06-15
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.