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- PDB-6tq8: Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): t... -

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Basic information

Entry
Database: PDB / ID: 6tq8
TitleAlcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): thermostable 10fold mutant
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: 2.5 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

Downloads & links

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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)103,3704
Polymers103,3704
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-58 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.671, 86.518, 102.751
Angle α, β, γ (deg.)90.000, 100.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
enzyme subunit


Mass: 25842.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Starmerella magnoliae (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): NEB 10-beta
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
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: 0.999998 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.5→49.16 Å / Num. obs: 29671 / % possible obs: 96 % / Redundancy: 4.5 % / CC1/2: 0.979 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.104 / Rrim(I) all: 0.232 / Net I/σ(I): 3.8 / Num. measured all: 133568 / Scaling rejects: 155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.64.81.1971635834120.6370.5621.3311.298.2
9.01-49.164.90.12331196330.9870.0580.1379.190.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TQ3

6tq3


Resolution: 2.5→19.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.553 / SU ML: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2881 842 2.9 %RANDOM
Rwork0.1887 ---
obs0.1915 28584 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 147.22 Å2 / Biso mean: 58.287 Å2 / Biso min: 29.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.04 Å2
2---0.19 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7116 0 0 137 7253
Biso mean---47 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0147238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176715
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.6429849
X-RAY DIFFRACTIONr_angle_other_deg0.8291.63615692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9415963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3923.217286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.725151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3051530
X-RAY DIFFRACTIONr_chiral_restr0.0520.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021251
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 69 -
Rwork0.34 2083 -
all-2152 -
obs--96.81 %

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