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), 0.182 (DCC)
R-Value Work:
0.132 (Depositor), 0.132 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.182 (DCC)
R-Value Work: 0.132 (Depositor), 0.132 (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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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

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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.