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- PDB-6tq3: Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA) -

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Basic information

Entry
Database: PDB / ID: 6tq3
TitleAlcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA)
ComponentsEnzyme subunit
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / thermal stability / protein engineering
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesStarmerella magnoliae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRovida, S. / Aalbers, F.S. / Fraaije, M.W. / Mattevi, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionH2020-LEIT BIO-2014-1 635734European Union
CitationJournal: Elife / Year: 2020
Title: Approaching boiling point stability of an alcohol dehydrogenase through computationally-guided enzyme engineering.
Authors: Aalbers, F.S. / Furst, M.J. / Rovida, S. / Trajkovic, M. / Gomez Castellanos, J.R. / Bartsch, S. / Vogel, A. / Mattevi, A. / Fraaije, M.W.
History
DepositionDec 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Enzyme subunit
B: Enzyme subunit
C: Enzyme subunit
D: Enzyme subunit


Theoretical massNumber of molelcules
Total (without water)102,6934
Polymers102,6934
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-55 kcal/mol
Surface area31860 Å2
Unit cell
Length a, b, c (Å)52.505, 87.245, 102.922
Angle α, β, γ (deg.)90.000, 101.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enzyme subunit


Mass: 25673.166 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Starmerella magnoliae (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% w/v PEG 3350, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 61616 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.054.50.7244860.7850.380.81798.6
8-44.34.70.0217220.9990.010.02399

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLN

5mln


Resolution: 2→44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.566 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.178
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1841 3 %RANDOM
Rwork0.1946 ---
obs0.1962 59755 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.77 Å2 / Biso mean: 39.283 Å2 / Biso min: 20.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å21.47 Å2
2--0.45 Å20 Å2
3----2.24 Å2
Refinement stepCycle: final / Resolution: 2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 0 394 7398
Biso mean---42.75 -
Num. residues----954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197161
X-RAY DIFFRACTIONr_bond_other_d0.0020.026951
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9619737
X-RAY DIFFRACTIONr_angle_other_deg1.063316020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085953
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28824.98251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.851151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3471527
X-RAY DIFFRACTIONr_chiral_restr0.1060.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021485
LS refinement shellResolution: 2→2.048 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.335 172 -
Rwork0.296 4312 -
obs--98.64 %

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