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- PDB-8zav: alcohol dehydrogenases KpADH mutant - S9Y/F161K -

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Basic information

Entry
Database: PDB / ID: 8zav
Titlealcohol dehydrogenases KpADH mutant - S9Y/F161K
ComponentsNAD-dependent epimerase/dehydratase domain-containing protein
KeywordsSTRUCTURAL PROTEIN / KpADH / Complex / Alcohol dehydrogenases
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 / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesVanderwaltozyma polyspora DSM 70294 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, L. / Ni, Y. / Xu, G.C.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Engineering alcohol dehydrogenases KpADH for enhanced organic-solvent tolerance and its molecular mechanisms
Authors: Zhang, L. / Ni, Y. / Xu, G.C.
History
DepositionApr 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase domain-containing protein
B: NAD-dependent epimerase/dehydratase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6256
Polymers78,0142
Non-polymers1,6114
Water1086
1
A: NAD-dependent epimerase/dehydratase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8133
Polymers39,0071
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-4 kcal/mol
Surface area14880 Å2
MethodPISA
2
B: NAD-dependent epimerase/dehydratase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8133
Polymers39,0071
Non-polymers8052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-4 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.440, 103.440, 134.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein NAD-dependent epimerase/dehydratase domain-containing protein


Mass: 39007.246 Da / Num. of mol.: 2 / Mutation: S9Y/F161K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora DSM 70294 (fungus)
Gene: Kpol_529p27 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7TM80
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Crystal Screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→48.34 Å / Num. obs: 17103 / % possible obs: 93.9 % / Redundancy: 3.6 % / CC1/2: 0.94 / Net I/σ(I): 4.8
Reflection shellResolution: 2.9→3.07 Å / Num. unique obs: 2824 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.34 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.813 / SU B: 27.147 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28837 875 5.1 %RANDOM
Rwork0.23931 ---
obs0.24179 16225 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.203 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-0.84 Å20 Å2
2---1.68 Å2-0 Å2
3---5.45 Å2
Refinement stepCycle: 1 / Resolution: 2.9→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 104 6 5608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195730
X-RAY DIFFRACTIONr_bond_other_d0.0010.025394
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9737772
X-RAY DIFFRACTIONr_angle_other_deg0.728312486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06425.662272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.503151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6561514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.8282734
X-RAY DIFFRACTIONr_mcbond_other0.6121.8282733
X-RAY DIFFRACTIONr_mcangle_it1.1362.743414
X-RAY DIFFRACTIONr_mcangle_other1.1362.743415
X-RAY DIFFRACTIONr_scbond_it0.3871.8492996
X-RAY DIFFRACTIONr_scbond_other0.3871.8492996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7592.7494359
X-RAY DIFFRACTIONr_long_range_B_refined1.9620.7356353
X-RAY DIFFRACTIONr_long_range_B_other1.95920.7376352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11434 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.974 Å
RfactorNum. reflection% reflection
Rfree0.37 84 -
Rwork0.365 1203 -
obs--95.83 %

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