3UF0 | pdb_00003uf0

Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)

PDB DOI: https://doi.org/10.2210/pdb3UF0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Beutenbergia cavernae DSM 12333
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-31 Released: 2011-11-23
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.195 (Depositor), 0.194 (DCC)
R-Value Work:
0.162 (Depositor), 0.161 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)

Vetting, M.W., Toro, R., Bhosle, R., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 57.53 kDa
Atom Count: 3,900
Modeled Residue Count: 498
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B	273	Beutenbergia cavernae DSM 12333	Mutation(s): 0 Gene Names: Bcav_0642 EC: 1.1.1.125
UniProt
Find proteins for C5BY10 (Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / CCUG 43141 / JCM 11478 / NBRC 16432 / NCIMB 13614 / HKI 0122)) Explore C5BY10 Go to UniProtKB: C5BY10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5BY10
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.195 (Depositor), 0.194 (DCC)
R-Value Work: 0.162 (Depositor), 0.161 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.47	α = 90
b = 115.47	β = 90
c = 76.182	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description