8YVW | pdb_00008yvw

Crystal structure of D12N mutant of L-azetidine-2-carboxylate hydrolase

• PDB DOI: https://doi.org/10.2210/pdb8YVW/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. A2C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-29 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.145 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.33 kDa 
• Atom Count: 2,561 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-2-haloacid dehalogenase	A	240	Pseudomonas sp. A2C	Mutation(s): 1  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
FMT (Subject of Investigation/LOI)	B [auth A], C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.145 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.176	α = 90
b = 71.361	β = 90
c = 72.349	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Toyoda, M., Mizutani, K., Mikami, B., Wackett, L.P., Esaki, N., Kurihara, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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