5YN4 | pdb_00005yn4

Crystal structure of dimeric peptidyl tRNA hydrolase from Acinetobacter baumannii with occluded substrate binding site at 1.47 A resolution

PDB DOI: https://doi.org/10.2210/pdb5YN4/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-24 Released: 2017-11-15
Deposition Author(s): Singh, P.K., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.170 (Depositor), 0.172 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of dimeric peptidyl tRNA hydrolase from Acinetobacter baumannii with occluded substrate binding site at 1.47 A resolution

Singh, P.K., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 41.94 kDa
Atom Count: 3,466
Modeled Residue Count: 386
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	193	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0 Gene Names: pth, F911_03144, HMPREF0010_01329 EC: 3.1.1.29
UniProt
Find proteins for D0C9L6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0C9L6 Go to UniProtKB: D0C9L6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0C9L6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.170 (Depositor), 0.172 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.556	α = 90
b = 98.08	β = 90
c = 123.812	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2023-11-22
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.