6FFX | pdb_00006ffx

Crystal structure of R. ruber ADH-A, mutant F43H

PDB DOI: https://doi.org/10.2210/pdb6FFX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus sp. M8
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2018-01-09 Released: 2018-02-14
Deposition Author(s): Dobritzsch, D., Maurer, D., Hamnevik, E., Enugala, T.R., Widersten, M.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.245 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Directed Evolution of Alcohol Dehydrogenase for Improved Stereoselective Redox Transformations of 1-Phenylethane-1,2-diol and Its Corresponding Acyloin.

Hamnevik, E., Maurer, D., Enugala, T.R., Chu, T., Lofgren, R., Dobritzsch, D., Widersten, M.

(2018) Biochemistry 57: 1059-1062

PubMed: 29384657 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.8b00055
Primary Citation Related Structures:
6FFX, 6FFZ

PubMed Abstract:
Laboratory evolution of alcohol dehydrogenase produced enzyme variants with improved turnover numbers with a vicinal 1,2-diol and its corresponding hydroxyketone. Crystal structure and transient kinetics analysis aids in rationalizing the new functions of these variants.

Organizational Affiliation

Department of Chemistry-BMC, Uppsala University , Box 576, SE-751 23 Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 147.54 kDa
Atom Count: 10,168
Modeled Residue Count: 1,384
Deposited Residue Count: 1,408
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase	A, B, C, D	352	Rhodococcus sp. M8	Mutation(s): 1 Gene Names: BKE56_025765

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.245 (DCC)
R-Value Work: 0.221 (Depositor), 0.221 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.647	α = 90
b = 103.162	β = 90.74
c = 111.187	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-02-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2018-02-14
Type: Initial release
Version 1.1: 2018-02-28
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description