7A6G | pdb_00007a6g

Structural characterization of L-proline amide hydrolase from Pseudomonas syringae

PDB DOI: https://doi.org/10.2210/pdb7A6G/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas syringae pv. tomato
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-25 Released: 2021-10-06
Deposition Author(s): Martinez-Rodriguez, S., Gavira, J.A.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.223 (Depositor), 0.204 (DCC)
R-Value Work:
0.156 (Depositor)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

A New L-Proline Amide Hydrolase with Potential Application within the Amidase Process

Martinez-Rodriguez, S., Contreras-Montoya, R., Torres, J.M., de Cienfuegos, L.A., Gavira, J.A.

(2022) Crystals (Basel) 12

DOI: https://doi.org/10.3390/cryst12010018

Macromolecule Content

Total Structure Weight: 36.85 kDa
Atom Count: 2,824
Modeled Residue Count: 303
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Proline iminopeptidase	A	328	Pseudomonas syringae pv. tomato	Mutation(s): 0 Gene Names: ALO36_01328

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.223 (Depositor), 0.204 (DCC)
R-Value Work: 0.156 (Depositor)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.428	α = 90
b = 65.033	β = 90
c = 85.016	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Martinez-Rodriguez, S.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BIO2016-74875-P

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2022-04-20
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, 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.