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- PDB-7fjg: Crystal structure of butanol dehydrogenase A (YqdH) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7fjg
TitleCrystal structure of butanol dehydrogenase A (YqdH) in complex with partial NADH from Fusobacterium nucleatum
ComponentsNADH-dependent butanol dehydrogenase A
KeywordsBIOSYNTHETIC PROTEIN / YqdH / partial NADH
Function / homology
Function and homology information


alcohol dehydrogenase [NAD(P)+] activity / methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) 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. / 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 subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsBai, X. / Lan, J. / Wang, L. / Bu, T. / Xu, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of butanol dehydrogenase A (YqdH) in complex with partial NADH from Fusobacterium nucleatum
Authors: Bai, X. / Lan, J. / Wang, L. / Bu, T. / Xu, Y.
History
DepositionAug 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)43,8193
Polymers43,3361
Non-polymers4832
Water27015
1
A: NADH-dependent butanol dehydrogenase A
hetero molecules

A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6386
Polymers86,6722
Non-polymers9664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4900 Å2
ΔGint-55 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.426, 79.351, 212.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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 subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355) (bacteria)
Gene: FN1415 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8R612, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.8M Ammonium phosphate monobasic, 0.1M HEPES 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: 0.9796 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.719→35.53 Å / Num. obs: 14933 / % possible obs: 98.53 % / Redundancy: 12.4 % / Biso Wilson estimate: 53.81 Å2 / Rsym value: 0.233 / Net I/σ(I): 11.875
Reflection shellResolution: 2.719→2.817 Å / Num. unique obs: 752 / Rsym value: 1.157

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→35.53 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4584
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2721 1493 10.01 %
Rwork0.2069 13427 -
obs0.2121 14933 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.07 Å2
Refinement stepCycle: LAST / Resolution: 2.72→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 28 15 3025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01483069
X-RAY DIFFRACTIONf_angle_d1.56124155
X-RAY DIFFRACTIONf_chiral_restr0.0663472
X-RAY DIFFRACTIONf_plane_restr0.0086523
X-RAY DIFFRACTIONf_dihedral_angle_d9.87921831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.810.35771180.2591068X-RAY DIFFRACTION87.82
2.81-2.910.3511340.23871203X-RAY DIFFRACTION100
2.91-3.020.31191350.22891215X-RAY DIFFRACTION100
3.02-3.160.31641350.24051214X-RAY DIFFRACTION100
3.16-3.330.34021360.21431222X-RAY DIFFRACTION99.93
3.33-3.540.29471360.20931222X-RAY DIFFRACTION99.93
3.54-3.810.28011380.18441242X-RAY DIFFRACTION100
3.81-4.190.27411360.17251223X-RAY DIFFRACTION100
4.19-4.80.18521380.17671245X-RAY DIFFRACTION99.93
4.8-6.040.25321400.2071260X-RAY DIFFRACTION100

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