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- PDB-9ugt: Structure of Butanol Dehydrogenase in Complex with ADP and Co -

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Basic information

Entry
Database: PDB / ID: 9ugt
TitleStructure of Butanol Dehydrogenase in Complex with ADP and Co
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
ADENOSINE-5'-DIPHOSPHATE / : / NADH-dependent butanol dehydrogenase A
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsBai, X. / Meng, D. / Nam, K.H. / Xu, Y.B.
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)43,8223
Polymers43,3361
Non-polymers4862
Water48627
1
A: NADH-dependent butanol dehydrogenase A
hetero molecules

A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6446
Polymers86,6722
Non-polymers9724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4930 Å2
ΔGint-51 kcal/mol
Surface area30400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.426, 79.351, 212.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
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: 2.7→50 Å / Num. obs: 14951 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.947 / Net I/σ(I): 11.875
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 725 / CC1/2: 0.707

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.72→35.49 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1469 9.99 %
Rwork0.2008 --
obs0.2056 14702 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 28 27 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d10.468417
X-RAY DIFFRACTIONf_chiral_restr0.057475
X-RAY DIFFRACTIONf_plane_restr0.009525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.820.35731280.28871156X-RAY DIFFRACTION86
2.82-2.930.34581430.25311279X-RAY DIFFRACTION96
2.93-3.060.32871440.23931301X-RAY DIFFRACTION97
3.06-3.230.30421460.251315X-RAY DIFFRACTION98
3.23-3.430.29941460.20631322X-RAY DIFFRACTION99
3.43-3.690.22371490.18861346X-RAY DIFFRACTION99
3.69-4.060.24361510.16611351X-RAY DIFFRACTION100
4.06-4.650.20291510.16771367X-RAY DIFFRACTION100
4.65-5.850.22051530.18431371X-RAY DIFFRACTION100

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