6IVV | pdb_00006ivv

Structure of peptidyl-tRNA hydrolase from Acinetobacter baumannii with multiple surface binding regions at 1.26A resolution

PDB DOI: https://doi.org/10.2210/pdb6IVV/pdb

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

Deposited: 2018-12-04 Released: 2018-12-19
Deposition Author(s): Viswanathan, V., Sharma, P., Chaudhary, A., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free:
0.184 (Depositor), 0.185 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure of peptide t-RNA hydrolase from Acinetobacter baumannii with multiple surface binding sites at 1.26 Angstrom resolution.

Singh, T.P., Viswanathan, V.

To be published.

Macromolecule Content

Total Structure Weight: 21.77 kDa
Atom Count: 1,743
Modeled Residue Count: 196
Deposited Residue Count: 196
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	196	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0 Gene Names: pth, 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.184 (Depositor), 0.185 (DCC)
R-Value Work: 0.158 (Depositor), 0.158 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.945	α = 90
b = 66.034	β = 90
c = 75.711	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Viswanathan, V.

Revision History (Full details and data files)

Version 1.0: 2018-12-19
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.