4BMV

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), 0.260 (DCC)
R-Value Work:
0.234 (Depositor), 0.240 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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
Modelled Residue Count: 2,562
Deposited Residue Count: 2,620
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9U359
Sequence Annotations Expand
Reference Sequence LOADING

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 K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain S [auth I] SDF format, chain T [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain S [auth I] MOL2 format, chain T [auth J] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain S [auth I] mmCIF format, chain T [auth J]	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), 0.260 (DCC)
R-Value Work: 0.234 (Depositor), 0.240 (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

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

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Help and Resources

4BMV

Short-chain dehydrogenase from Sphingobium yanoikuyae in complex with NADPH

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)