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- PDB-8ee3: F93Y Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 8ee3
TitleF93Y Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
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 Rossmann-like Domain ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZheng, C. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: To Be Published
Title: Structure of F93Y horse liver alcohol dehydrogenase at 1.55 Angstroms resolution
Authors: Zheng, C. / Boxer, S.G.
History
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,95610
Polymers80,1092
Non-polymers1,8478
Water19,1861065
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-108 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.328, 50.681, 92.930
Angle α, β, γ (deg.)92.490, 102.960, 109.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 40054.453 Da / Num. of mol.: 2 / Mutation: F93Y
Source method: isolated from a genetically manipulated source
Details: liver enzyme / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400 (10%-25%), 2mM NADH, 10mM N-cyclohexylformamide in Tris buffer at pH 8.20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→39.98 Å / Num. obs: 99050 / % possible obs: 91.5 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Net I/σ(I): 12.6 / Num. measured all: 376420 / Scaling rejects: 215
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
1.55-1.573.20.731294540980.640.4830.881.476.8
8.47-39.983.90.02624666360.9990.0150.0346.796.8

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RM6

7rm6


Resolution: 1.55→39.98 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.183 4949 5 %
Rwork0.1632 94054 -
obs0.1642 99003 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.76 Å2 / Biso mean: 22.037 Å2 / Biso min: 10.71 Å2
Refinement stepCycle: final / Resolution: 1.55→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 110 1065 6747
Biso mean--17.45 33.4 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.560.32041230.34882336245970
1.56-1.580.26861700.28853228339892
1.58-1.60.29461620.26233092325492
1.6-1.620.29521660.25483137330392
1.62-1.640.26771670.22733163333091
1.64-1.660.25131610.2233072323391
1.66-1.690.2441660.21383145331190
1.69-1.710.23371620.19943074323690
1.71-1.740.21311570.19162975313288
1.74-1.770.24361560.19032976313286
1.77-1.80.22221430.18062724286779
1.8-1.830.20711660.17683158332493
1.83-1.870.18591720.17413252342495
1.87-1.910.17551680.16923220338894
1.91-1.950.20231730.17153278345195
1.95-1.990.20861690.17113211338095
1.99-2.040.1981710.16973243341494
2.04-2.10.18171690.16113245341494
2.1-2.160.18661690.16413209337894
2.16-2.230.19091690.16133217338694
2.23-2.310.19421690.16073198336793
2.31-2.40.17881650.15733134329992
2.4-2.510.17161530.16312917307086
2.51-2.640.16771660.163140330692
2.64-2.810.15861760.16883337351397
2.81-3.020.18531740.16073307348197
3.02-3.330.17961740.1583323349797
3.33-3.810.15231720.14463260343296
3.81-4.80.15431660.1283156332291
4.8-39.980.14631750.1333327350297

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