9OER | pdb_00009oer

HalA with lysine, Fe(II), chloride, and a peroxyhemiketal intermediate

PDB DOI: https://doi.org/10.2210/pdb9OER/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Actinoplanes teichomyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-11-19
Deposition Author(s): Kissman, E.N., Yang, A.Y., 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: 1.72 Å
R-Value Free:
0.201 (Depositor), 0.203 (DCC)
R-Value Work:
0.168 (Depositor), 0.171 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

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: 241.59 kDa
Atom Count: 16,420
Modeled Residue Count: 2,014
Deposited Residue Count: 2,064
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, E A, B, C, D, E, F, G, H	258	Actinoplanes teichomyceticus	Mutation(s): 0 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YL0 (Subject of Investigation/LOI) Query on YL0 Download Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain GA [auth G] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain GA [auth G] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	GA [auth G], Q [auth C], U [auth D]	(4R)-4-chloro-L-lysine C₆ H₁₃ Cl N₂ O₂ RARMVOFXKPZWMG-UHNVWZDZSA-N		Interactions Focus chain GA [auth G] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain GA [auth G] Focus chain Q [auth C] Focus chain U [auth D]
A1CA1 (Subject of Investigation/LOI) Query on A1CA1 Download Ideal Coordinates CCD File SDF format, chain Z [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain Z [auth E]	Z [auth E]	(2S)-2-hydroperoxy-2-hydroxypentanedioic acid C₅ H₈ O₇ IHRVEKFTFSYRQQ-YFKPBYRVSA-N		Interactions Focus chain Z [auth E] Interactions & Density Focus chain Z [auth E]
LYS (Subject of Investigation/LOI) Query on LYS Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain KA [auth H] SDF format, chain M [auth B] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth E]	CA [auth F], I [auth A], KA [auth H], M [auth B], Y [auth E]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain KA [auth H] Focus chain M [auth B] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain KA [auth H] Focus chain M [auth B] Focus chain Y [auth E]
AKG (Subject of Investigation/LOI) Query on AKG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth D] MOL2 format, chain J [auth A] MOL2 format, chain V [auth D] mmCIF format, chain J [auth A] mmCIF format, chain V [auth D]	J [auth A], V [auth D]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain V [auth D] Interactions & Density Focus chain J [auth A] Focus chain V [auth D]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain LA [auth H] SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C]	DA [auth F], HA [auth G], LA [auth H], N [auth B], R [auth C]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C]
FE2 (Subject of Investigation/LOI) Query on FE2 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain K [auth A] SDF format, chain MA [auth H] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain O [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain O [auth B]	AA [auth E] EA [auth F] IA [auth G] K [auth A] MA [auth H] AA [auth E], EA [auth F], IA [auth G], K [auth A], MA [auth H], O [auth B], S [auth C], W [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain JA [auth G] SDF format, chain L [auth A] SDF format, chain NA [auth H] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	BA [auth E] FA [auth F] JA [auth G] L [auth A] NA [auth H] BA [auth E], FA [auth F], JA [auth G], L [auth A], NA [auth H], P [auth B], T [auth C], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.201 (Depositor), 0.203 (DCC)
R-Value Work: 0.168 (Depositor), 0.171 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.3	α = 90
b = 147.3	β = 90
c = 287.87	γ = 120

Software Package:

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

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.

Yang, A.Y.

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