7XTO

Structure of ClA2 reveal the Mechanism of soil bacterial derived chlorinase

PDB DOI: https://doi.org/10.2210/pdb7XTO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Umezawaea tangerina
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2022-05-17 Released: 2023-01-25
Deposition Author(s): Liu, Y.H., Liu, Y., Li, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.304
R-Value Work: 0.278
R-Value Observed: 0.280

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Expression, purification and structure determination of the chlorinase ClA2.

Liu, Y., Zhang, H., Xiao, H., Li, Y., Liu, Y.

(2022) Biochem Biophys Res Commun 628: 64-67

PubMed: 36081280 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2022.08.081
Primary Citation of Related Structures:
7XTO

PubMed Abstract:
Halogenated compounds are particularly important in pharmaceutical and agrochemical products. Biochemical halogenation with halogenases are environmental friendly reactions with high efficiency. Recently, the two new chlorinases (ClA1 and ClA2) were discovered from soil bacteria. However, the protein structure of ClA2 was not identified. Here, we determined the high-resolution crystal structure of ClA2. This structure will help us to understand the catalytic mechanism of chlorinase, and explain the catalytic process of the coupled chlorinase-fluorinase system, which offers the prospect of arising rapid radiolabeling protocols under mild conditions.

Organizational Affiliation

Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, China.

Macromolecule Content

Total Structure Weight: 175.89 kDa
Atom Count: 10,672
Modelled Residue Count: 1,484
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
soil bacterial derived chlorinase	A B [auth C] C [auth D] D [auth B] E A, B [auth C], C [auth D], D [auth B], E, F	276	Umezawaea tangerina	Mutation(s): 0 Gene Names: CLV43_107328
UniProt
Find proteins for A0A2T0T269 (Umezawaea tangerina) Explore A0A2T0T269 Go to UniProtKB: A0A2T0T269
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T0T269
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1DA Query on 1DA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth B] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F]	G [auth A] H [auth C] I [auth D] J [auth B] K [auth E] G [auth A], H [auth C], I [auth D], J [auth B], K [auth E], L [auth F]	1-DEAZA-ADENOSINE C₁₁ H₁₄ N₄ O₄ NVUDDRWKCUAERS-PNHWDRBUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.304
R-Value Work: 0.278
R-Value Observed: 0.280
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.378	α = 90
b = 104.423	β = 108.88
c = 124.966	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Liu, Y.H.

Liu, Y.

Li, Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82172299

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-08-09
Changes: Database references, Refinement description
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description