5OD3 | pdb_00005od3

Crystal structure of R. ruber ADH-A, mutant Y54G, L119Y

PDB DOI: https://doi.org/10.2210/pdb5OD3/pdb

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

Deposited: 2017-07-04 Released: 2018-07-04
Deposition Author(s): Dobritzsch, D., Maurer, D., Hamnevik, E., Enugala, T.R., Widersten, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.169 (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

Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases

Maurer, D., Enugala, T.R., Hamnevik, E., Bauer, P., Luking, M., Petrovic, D., Hillier, H., Kamerlin, S.C.L., Dobritzsch, D., Widersten, M.

(2018) ACS Catal 8

DOI: https://doi.org/10.1021/acscatal.8b01762

Macromolecule Content

Total Structure Weight: 147.35 kDa
Atom Count: 11,286
Modeled Residue Count: 1,381
Deposited Residue Count: 1,408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase	A, B, C, D	352	Rhodococcus sp. M8	Mutation(s): 2 Gene Names: BKE56_025765
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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 G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	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 E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	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: 1.83 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.168 (Depositor), 0.180 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.555	α = 90
b = 105.969	β = 91.37
c = 108.076	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

Entry History

Deposition Data

Released Date: 2018-07-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-04
Type: Initial release
Version 1.1: 2018-08-22
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description