8YWO | pdb_00008ywo

Crystal structure of L-azetidine-2-carboxylate hydrolase soaked in (S)-azetidine-2-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb8YWO/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas sp. A2C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-31 Released: 2024-05-08
Deposition Author(s): Toyoda, M., Mizutani, K., Mikami, B., Wackett, L.P., Esaki, N., Kurihara, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.132 (Depositor), 0.130 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Research for the crystal structure of L-azetidine-2-carboxylate hydrolase

Toyoda, M., Jitsumori, K., Mikami, B., Mizutani, K., Esaki, N., Wackett, L.P., Kurihara, T.

To be published.

Macromolecule Content

Total Structure Weight: 27.25 kDa
Atom Count: 2,374
Modeled Residue Count: 240
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-2-haloacid dehalogenase	A	240	Pseudomonas sp. A2C	Mutation(s): 0 EC: 3.8.1.2 (PDB Primary Data), 3.5 (UniProt)
UniProt
Find proteins for B2Z3V8 (Pseudomonas sp. (strain A2C)) Explore B2Z3V8 Go to UniProtKB: B2Z3V8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2Z3V8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
02A (Subject of Investigation/LOI) Query on 02A 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]	(2S)-azetidine-2-carboxylic acid C₄ H₇ N O₂ IADUEWIQBXOCDZ-VKHMYHEASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.132 (Depositor), 0.130 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.105	α = 90
b = 64.419	β = 106.99
c = 54.307	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release

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.