4BMV | pdb_00004bmv

Short-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH

PDB DOI: https://doi.org/10.2210/pdb4BMV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sphingobium yanoikuyae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-10 Released: 2014-03-19
Deposition Author(s): Man, H., Kedziora, K., Lavandera-Garcia, I., Gotor-Fernandez, V., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.251 (Depositor), 0.259 (DCC)
R-Value Work:
0.234 (Depositor), 0.241 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 286.45 kDa
Atom Count: 19,692
Modeled Residue Count: 2,562
Deposited Residue Count: 2,620
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHORT-CHAIN DEHYDROGENASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	262	Sphingobium yanoikuyae	Mutation(s): 0 EC: 1.1.1.1
UniProt
Find proteins for B9U359 (Sphingobium yanoikuyae) Explore B9U359 Go to UniProtKB: B9U359
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9U359
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain T [auth J] SDF format, chain S [auth I] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth J] MOL2 format, chain S [auth I] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth J] mmCIF format, chain S [auth I] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A] L [auth B] M [auth C] N [auth D] O [auth E] K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.251 (Depositor), 0.259 (DCC)
R-Value Work: 0.234 (Depositor), 0.241 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.91	α = 90
b = 86.84	β = 106.36
c = 155.61	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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

4BMV | pdb_00004bmv

Short-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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