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- PDB-8z6z: Medium-chain dehydrogenase/reductase MrADH-WT -

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Basic information

Entry
Database: PDB / ID: 8z6z
TitleMedium-chain dehydrogenase/reductase MrADH-WT
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: 2.59 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)36,0834
Polymers35,2891
Non-polymers7943
Water2,180121
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)144,33416
Polymers141,1574
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 area14790 Å2
ΔGint-265 kcal/mol
Surface area45510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.120, 96.120, 199.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

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Components

#1: Protein alcohol dehydrogenase


Mass: 35289.133 Da / Num. of mol.: 1
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.: 121 / 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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tris-HCl, PEG 4000

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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: Mar 6, 2023 / Details: multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.59→43.28 Å / Num. obs: 17662 / % possible obs: 100 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.076 / Net I/σ(I): 13.1
Reflection shellResolution: 2.59→2.71 Å / Rmerge(I) obs: 1.066 / Num. unique obs: 2091 / Rpim(I) all: 0.518

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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: 2.59→43.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.251 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24041 843 4.8 %RANDOM
Rwork0.19757 ---
obs0.19965 16819 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.314 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å20 Å2
2--1.28 Å2-0 Å2
3----4.14 Å2
Refinement stepCycle: 1 / Resolution: 2.59→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 46 121 2646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192584
X-RAY DIFFRACTIONr_bond_other_d0.0010.022453
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9943532
X-RAY DIFFRACTIONr_angle_other_deg0.773.0025620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7422.79693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5941520
X-RAY DIFFRACTIONr_chiral_restr0.0650.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
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_it1.5343.9861379
X-RAY DIFFRACTIONr_mcbond_other1.5253.9871378
X-RAY DIFFRACTIONr_mcangle_it2.4845.9761722
X-RAY DIFFRACTIONr_mcangle_other2.4865.9761723
X-RAY DIFFRACTIONr_scbond_it2.1584.2161204
X-RAY DIFFRACTIONr_scbond_other2.144.2151204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1726.2341811
X-RAY DIFFRACTIONr_long_range_B_refined4.66247.4172770
X-RAY DIFFRACTIONr_long_range_B_other4.61647.4022742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 67 -
Rwork0.284 1200 -
obs--100 %

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