4DHW | pdb_00004dhw

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Adipic acid at 2.4 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4DHW/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-30 Released: 2012-02-29
Deposition Author(s): Kumar, A., Singh, A., Singh, N., Sinha, M., Sharma, S., Arora, A., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.206 (Depositor), 0.283 (DCC)
R-Value Work:
0.195 (Depositor), 0.192 (DCC)

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

Literature

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Adipic acid at 2.4 Angstrom resolution

Kumar, A., Singh, A., Singh, N., Sinha, M., Sharma, S., Arora, A., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 41.96 kDa
Atom Count: 3,142
Modeled Residue Count: 388
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	194	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA4672, pth EC: 3.1.1.29
UniProt
Find proteins for Q9HVC3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVC3 Go to UniProtKB: Q9HVC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HVC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0L1 Query on 0L1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	hexanedioic acid C₆ H₁₀ O₄ WNLRTRBMVRJNCN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.206 (Depositor), 0.283 (DCC)
R-Value Work: 0.195 (Depositor), 0.192 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.594	α = 90
b = 64.594	β = 90
c = 156.245	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.