7A6G

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
R-Value Work: 0.156
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 303
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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]	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
R-Value Work: 0.156
R-Value Observed: 0.160
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

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.