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- PDB-8z6y: Medium-chain dehydrogenase/reductase MrADH mutant-V164K&V221A&H333K -

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Basic information

Entry
Database: PDB / ID: 8z6y
TitleMedium-chain dehydrogenase/reductase MrADH mutant-V164K&V221A&H333K
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Medium-chain dehydrogenase/reductase / ketone / secondary alcohol
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / alcohol dehydrogenase
Similarity search - Component
Biological speciesModestobacter roseus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsXue, J.Y. / Xu, G.C. / Ni, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22378169 China
CitationJournal: To Be Published
Title: Enhancing the solubility and elucidating the mechanisms of the highly stereoselective oxidoreductase MrADH: an insight from molecular dynamics simulations
Authors: Xue, J.Y. / Xu, G.C. / Ni, Y.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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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)36,0764
Polymers35,2821
Non-polymers7943
Water19811
1
A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,30616
Polymers141,1294
Non-polymers3,17712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area14980 Å2
ΔGint-270 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.690, 95.690, 199.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein alcohol dehydrogenase


Mass: 35282.164 Da / Num. of mol.: 1 / Mutation: V164K,V221A,H333K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Modestobacter roseus (bacteria) / Gene: JD78_02120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A562IS02, alcohol dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Imidazole, PEG 20000, Isopropanol

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 21, 2023 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.87→47.85 Å / Num. obs: 12964 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.067 / Net I/σ(I): 13
Reflection shellResolution: 2.87→3.03 Å / Rmerge(I) obs: 1.047 / Num. unique obs: 1832 / Rpim(I) all: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→47.85 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 19.276 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.683 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26668 644 5 %RANDOM
Rwork0.21634 ---
obs0.21888 12314 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.115 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å21.52 Å2-0 Å2
2--3.04 Å2-0 Å2
3----9.86 Å2
Refinement stepCycle: 1 / Resolution: 2.87→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 46 11 2535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192582
X-RAY DIFFRACTIONr_bond_other_d0.0010.022460
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9973526
X-RAY DIFFRACTIONr_angle_other_deg0.7223.0025639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3422.82692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5421520
X-RAY DIFFRACTIONr_chiral_restr0.0590.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212945
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
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_it2.156.861378
X-RAY DIFFRACTIONr_mcbond_other2.156.861377
X-RAY DIFFRACTIONr_mcangle_it3.44910.2891721
X-RAY DIFFRACTIONr_mcangle_other3.44910.2891722
X-RAY DIFFRACTIONr_scbond_it2.5597.1621203
X-RAY DIFFRACTIONr_scbond_other2.5117.1591203
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.55310.6321805
X-RAY DIFFRACTIONr_long_range_B_refined5.29582.2182693
X-RAY DIFFRACTIONr_long_range_B_other5.29482.2042694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.873→2.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 51 -
Rwork0.345 877 -
obs--100 %

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