9OEW | pdb_00009oew

HalA N224V with lysine, succinate, chloride, and vanadium(IV)-oxo

PDB DOI: https://doi.org/10.2210/pdb9OEW/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Actinoplanes teichomyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-04-29 Released: 2025-11-19
Deposition Author(s): Kissman, E.N., Stone, E.A., Chang, M.C.Y.
Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.282 (Depositor), 0.284 (DCC)
R-Value Work:
0.231 (Depositor), 0.234 (DCC)
R-Value Observed:
0.233 (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

Dynamic metal coordination controls chemoselectivity in a radical halogenase

Kissman, E.N., Kipouros, I., Slater, J.W., Stone, E.A., Yang, A.Y., Braun, A., Ensberg, A.R., Whitten, A.M., Chatterjee, K., Bogacz, I., Yano, J., Bollinger Jr, J.M., Chang, M.C.Y.

To be published.

Macromolecule Content

Total Structure Weight: 120.62 kDa
Atom Count: 7,738
Modeled Residue Count: 996
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine halogenase	A, B, C, D	258	Actinoplanes teichomyceticus	Mutation(s): 1 Gene Names: FHX34_1011265
UniProt
Find proteins for A0A561WR11 (Actinoplanes teichomyceticus) Explore A0A561WR11 Go to UniProtKB: A0A561WR11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A561WR11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D]	E [auth A], I [auth B], M [auth C], Q [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
VVO (Subject of Investigation/LOI) Query on VVO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	oxovanadium(2+) O V MHHDXUNFNAZUGB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
V (Subject of Investigation/LOI) Query on V Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	K [auth B], O [auth C], S [auth D]	VANADIUM ION V KOKKJWHERHSKEB-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.282 (Depositor), 0.284 (DCC)
R-Value Work: 0.231 (Depositor), 0.234 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.557	α = 90
b = 146.557	β = 90
c = 287.265	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Kissman, E.N.

Stone, E.A.

Chang, M.C.Y.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DOE/LBL DEAC02-05CH11231 FWP CH030201
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM134271