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- PDB-7v1r: Leifsonia Alcohol Dehydrogenases LnADH -

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Basic information

Entry
Database: PDB / ID: 7v1r
TitleLeifsonia Alcohol Dehydrogenases LnADH
ComponentsAlcohol DehydrogenasesAlcohol dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / Alcohol / Dehydrogenases
Function / homologyISOPROPYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesLeifsonia antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSong, Y. / Qu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970054 China
CitationJournal: Chembiochem / Year: 2021
Title: Engineering Leifsonia Alcohol Dehydrogenase for Thermostability and Catalytic Efficiency by Enhancing Subunit Interactions.
Authors: Zhu, L. / Song, Y. / Chang, C. / Ma, H. / Yang, L. / Deng, Z. / Deng, W. / Qu, X.
History
DepositionAug 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol Dehydrogenases
B: Alcohol Dehydrogenases
C: Alcohol Dehydrogenases
D: Alcohol Dehydrogenases
E: Alcohol Dehydrogenases
F: Alcohol Dehydrogenases
G: Alcohol Dehydrogenases
H: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,20842
Polymers201,2438
Non-polymers6,96634
Water55831
1
A: Alcohol Dehydrogenases
B: Alcohol Dehydrogenases
D: Alcohol Dehydrogenases
E: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,17022
Polymers100,6214
Non-polymers3,54818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-295 kcal/mol
Surface area28500 Å2
MethodPISA
2
C: Alcohol Dehydrogenases
F: Alcohol Dehydrogenases
G: Alcohol Dehydrogenases
H: Alcohol Dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,03920
Polymers100,6214
Non-polymers3,41716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20010 Å2
ΔGint-322 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.944, 237.485, 68.784
Angle α, β, γ (deg.)90.000, 113.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alcohol Dehydrogenases / Alcohol dehydrogenase


Mass: 25155.346 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leifsonia antarctica (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate/Acetic acid, pH 7.0, 0.2M Zinc acetate, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 38243 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.498 / Num. unique obs: 1927

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7v1q

7v1q


Resolution: 2.81→49.49 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2949 1921 5 %RANDOM
Rwork0.2461 ---
obs0.2486 36281 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.41 Å2 / Biso mean: 29.905 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å2-0.33 Å2
2--0.45 Å20 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 2.81→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13927 0 402 31 14360
Biso mean--30.46 18.76 -
Num. residues----2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314606
X-RAY DIFFRACTIONr_bond_other_d0.0380.01713502
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.61919980
X-RAY DIFFRACTIONr_angle_other_deg2.4751.56430963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33152007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30523.409569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.809151924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2691556
X-RAY DIFFRACTIONr_chiral_restr0.0610.22015
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217091
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022901
LS refinement shellResolution: 2.81→2.879 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.367 138 -
Rwork0.307 2259 -
obs--82.8 %

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