4BMN | pdb_00004bmn

apo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428

PDB DOI: https://doi.org/10.2210/pdb4BMN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ralstonia sp. DSMZ 6428
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-10 Released: 2014-03-19
Deposition Author(s): Man, H., Kulig, J., Rother, D., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.188 (Depositor), 0.196 (DCC)
R-Value Work:
0.158 (Depositor), 0.170 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones

Man, H., Kedziora, K., Kulig, J., Frank, A., Lavandera, I., Gotor-Fernandez, V., Rother, D., Hart, S., Turkenburg, J.P., Grogan, G.

(2014) Top Catal 57: 356

DOI: https://doi.org/10.1007/S11244-013-0191-2

Macromolecule Content

Total Structure Weight: 109.12 kDa
Atom Count: 7,832
Modeled Residue Count: 929
Deposited Residue Count: 1,012
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALCLOHOL DEHYDROGENASE/SHORT-CHAIN DEHYDROGENASE	A, B, C, D	253	Ralstonia sp. DSMZ 6428	Mutation(s): 0 EC: 1.1.1.1
UniProt
Find proteins for C0IR58 (Ralstonia sp. DSMZ 6428) Explore C0IR58 Go to UniProtKB: C0IR58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0IR58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth B] G [auth B] I [auth C] J [auth C] E [auth A], F [auth B], G [auth B], I [auth C], J [auth C], K [auth D], L [auth D], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.188 (Depositor), 0.196 (DCC)
R-Value Work: 0.158 (Depositor), 0.170 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.48	α = 90
b = 52.51	β = 116.57
c = 151.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-19
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

4BMN | pdb_00004bmn

apo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428

Literature

Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium Spp. Reveal the Molecular Basis for Their Recognition of 'Bulky-Bulky' Ketones

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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