7QY3 | pdb_00007qy3

Crystal structure of the halohydrin dehalogenase HheG D114C mutant cross-linked with BMOE

PDB DOI: https://doi.org/10.2210/pdb7QY3/pdb

Classification: LYASE
Organism(s): Ilumatobacter coccineus YM16-304
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-01-27 Released: 2022-03-09
Deposition Author(s): Henke, S., Blankenfeldt, W., Schallmey, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.252 (Depositor), 0.218 (DCC)
R-Value Work:
0.211 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Biocatalytically active and stable cross-linked enzyme crystals of halohydrin dehalogenase HheG by protein engineering

Staar, M., Henke, S., Blankenfeldt, W., Schallmey, A.

(2022) ChemCatChem

DOI: https://doi.org/10.1002/cctc.202200145

Macromolecule Content

Total Structure Weight: 303.12 kDa
Atom Count: 19,012
Modeled Residue Count: 2,567
Deposited Residue Count: 2,820
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	282	Ilumatobacter coccineus YM16-304	Mutation(s): 1 Gene Names: YM304_35350
UniProt
Find proteins for A0A6C7EF96 (Ilumatobacter coccineus (strain NBRC 103263 / KCTC 29153 / YM16-304)) Explore A0A6C7EF96 Go to UniProtKB: A0A6C7EF96
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6C7EF96
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ME7 (Subject of Investigation/LOI) Query on ME7 Download:Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain OA [auth I] SDF format, chain LA [auth H] MOL2 format, chain HA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain LA [auth H] mmCIF format, chain HA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain LA [auth H]	HA [auth G], K [auth A], LA [auth H], OA [auth I], Q [auth B]	1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) C₁₀ H₈ N₂ O₄ PUKLCKVOVCZYKF-UHFFFAOYSA-N		Interactions Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain OA [auth I] Focus chain Q [auth B] Interactions & Density Focus chain HA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain OA [auth I] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain JA [auth G] SDF format, chain MA [auth H] SDF format, chain PA [auth I] SDF format, chain QA [auth I] SDF format, chain SA [auth J] SDF format, chain TA [auth J] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain X [auth D] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain RA [auth I] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth H] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth G] SDF format, chain IA [auth G] SDF format, chain GA [auth F] SDF format, chain BA [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain SA [auth J] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth D] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain BA [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain PA [auth I] mmCIF format, chain QA [auth I] mmCIF format, chain SA [auth J] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth D] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain BA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] EA [auth F] AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth F], FA [auth F], GA [auth F], IA [auth G], JA [auth G], KA [auth G], L [auth A], M [auth A], MA [auth H], N [auth A], NA [auth H], O [auth A], P [auth A], PA [auth I], QA [auth I], R [auth B], RA [auth I], S [auth B], SA [auth J], T [auth B], TA [auth J], U [auth C], V [auth C], W [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.252 (Depositor), 0.218 (DCC)
R-Value Work: 0.211 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.08	α = 90
b = 195.08	β = 90
c = 195.064	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-09

Deposition Author(s):

Henke, S.

Blankenfeldt, W.

Schallmey, A.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	281361126/GRK2223
German Research Foundation (DFG)	Germany	SPP 1934, SCHA 1745/2-2

Revision History (Full details and data files)

Version 1.0: 2022-03-09
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 2.0: 2025-10-01
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary