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- PDB-9ugs: Butanol Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 9ugs
TitleButanol Dehydrogenase
ComponentsNADH-dependent butanol dehydrogenase A
KeywordsBIOSYNTHETIC PROTEIN / National Butanol Dehydrogenase
Function / homology
Function and homology information


butanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / : / Fe-containing alcohol dehydrogenase family, C-terminal / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / NADH-dependent butanol dehydrogenase A
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBai, X. / Meng, D. / Xu, Y.B. / Nam, K.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF- 2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: To Be Published
Title: Flexibility of the Nicotinamide Group of the NADP Cofactor in Butanol Dehydrogenase YqdH from Fusobacterium nucleatum
Authors: Bai, X. / Xu, Y.B. / Nam, K.H.
History
DepositionApr 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3952
Polymers43,3361
Non-polymers591
Water2,684149
1
A: NADH-dependent butanol dehydrogenase A
hetero molecules

A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7904
Polymers86,6722
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3830 Å2
ΔGint-45 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.056, 78.916, 215.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

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Components

#1: Protein NADH-dependent butanol dehydrogenase A


Mass: 43336.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1415 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R612, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: 1.8M ammonium phosphate monobasic, 0.1M HEPES sodium salt pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19608 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.963 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 962 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→27.83 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1931 9.99 %
Rwork0.1849 --
obs0.1903 19336 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 1 149 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d0.93
X-RAY DIFFRACTIONf_dihedral_angle_d5.364412
X-RAY DIFFRACTIONf_chiral_restr0.051474
X-RAY DIFFRACTIONf_plane_restr0.009533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.31181270.23471152X-RAY DIFFRACTION94
2.56-2.630.2491360.21061214X-RAY DIFFRACTION98
2.63-2.710.2381350.18641224X-RAY DIFFRACTION98
2.71-2.80.25461360.1891210X-RAY DIFFRACTION99
2.8-2.90.25151360.20071232X-RAY DIFFRACTION99
2.9-3.010.26811370.20281231X-RAY DIFFRACTION98
3.01-3.150.25171380.20591240X-RAY DIFFRACTION99
3.15-3.310.29881380.20481252X-RAY DIFFRACTION99
3.31-3.520.25811390.18831247X-RAY DIFFRACTION99
3.52-3.790.26281400.17411253X-RAY DIFFRACTION100
3.79-4.170.20051420.15541271X-RAY DIFFRACTION100
4.17-4.770.20151400.14921269X-RAY DIFFRACTION99
4.78-6.010.19531430.18531287X-RAY DIFFRACTION99

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