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- PDB-7c3v: Structure of a thermostable Alcohol dehydrogenase from Kluyveromy... -

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Basic information

Entry
Database: PDB / ID: 7c3v
TitleStructure of a thermostable Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / thermostable
Function / homology: / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Alcohol dehydrogenase
Function and homology information
Biological speciesKluyveromyces sp. CCTCC M2011385 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20042955034 Å
AuthorsDai, W. / Ni, Y. / Xu, G. / Liu, Y. / Wang, Y. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: To Be Published
Title: Structure of a thermostable Alcohol dehydrogenase from Kluyveromyces polyspora(KpADH)
Authors: Dai, W. / Ni, Y. / Xu, G. / Liu, Y. / Wang, Y. / Zhou, J.
#1: Journal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Insight into Enantioselective Inversion of an Alcohol Dehydrogenase Reveals a "Polar Gate" in Stereorecognition of Diaryl Ketones.
Authors: Zhou, J. / Wang, Y. / Xu, G. / Wu, L. / Han, R. / Schwaneberg, U. / Rao, Y. / Zhao, Y.L. / Zhou, J. / Ni, Y.
History
DepositionMay 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6462
Polymers38,9031
Non-polymers7431
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.867, 102.867, 65.908
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

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Components

#1: Protein Alcohol dehydrogenase


Mass: 38903.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces sp. CCTCC M2011385 (yeast)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1B0UHJ2
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH7.2 36% PEG8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→24.71 Å / Num. obs: 18868 / % possible obs: 93.1 % / Redundancy: 5 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 2.79
Reflection shellResolution: 2.2→10 Å / Rmerge(I) obs: 0.058 / Num. unique obs: 18868

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z2X

5z2x


Resolution: 2.20042955034→24.7078541962 Å / SU ML: 0.267011207907 / Cross valid method: FREE R-VALUE / σ(F): 1.33750969307 / Phase error: 23.0290082545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230901236109 953 5.05087979648 %
Rwork0.186378116785 17915 -
obs0.188526221083 18868 93.0512403215 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.9609593147 Å2
Refinement stepCycle: LAST / Resolution: 2.20042955034→24.7078541962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 48 179 2969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004223873718392855
X-RAY DIFFRACTIONf_angle_d0.7491033871833877
X-RAY DIFFRACTIONf_chiral_restr0.0460294630405434
X-RAY DIFFRACTIONf_plane_restr0.00477867510687496
X-RAY DIFFRACTIONf_dihedral_angle_d9.400226665891716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.31640.3609995491151110.2781260856611957X-RAY DIFFRACTION72.131147541
2.3164-2.46140.3207316067141470.2427606259472319X-RAY DIFFRACTION85.1519337017
2.4614-2.65120.2123304419181560.215435351232556X-RAY DIFFRACTION94.4289693593
2.6512-2.91760.2692163832461190.2088735045382767X-RAY DIFFRACTION99.7925311203
2.9176-3.33890.2430086243311510.188136365732717X-RAY DIFFRACTION99.860724234
3.3389-4.20330.1996973903741370.1606700182342771X-RAY DIFFRACTION100
4.2033-24.70.1812866740911320.1574411851992828X-RAY DIFFRACTION99.8650472335

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