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- PDB-8ecs: F93G Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 8ecs
TitleF93G 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
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: 1.2 Å
AuthorsZheng, C. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: To Be Published
Title: Structure of F93G horse liver alcohol dehydrogenase at 1.20 Angstroms resolution
Authors: Zheng, C. / Mathews, I.I. / Boxer, S.G.
History
DepositionSep 2, 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

Downloads & links

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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)81,74410
Polymers79,8972
Non-polymers1,8478
Water17,619978
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-109 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.100, 50.280, 92.570
Angle α, β, γ (deg.)92.750, 102.880, 108.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39948.332 Da / Num. of mol.: 2 / Mutation: F93G
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.: 978 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
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: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2020
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→37.75 Å / Num. obs: 211968 / % possible obs: 92.5 % / Redundancy: 6.795 % / Biso Wilson estimate: 20.144 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 0.896 / Net I/σ(I): 11.8 / Num. measured all: 1440286 / Scaling rejects: 305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.235.2641.0811.396457416927122680.7791.272.5
1.23-1.265.6620.9921.648074116511142590.8061.09386.4
1.26-1.36.1430.8182.118837816051143870.8660.89389.6
1.3-1.346.9060.7032.629917115619143610.9150.75991.9
1.34-1.387.0170.5583.339840115087140240.9450.60393
1.38-1.437.1860.4644.099866714650137300.960.593.7
1.43-1.487.0080.3615.059286814114132510.9720.3993.9
1.48-1.557.2220.2736.599227013539127770.9840.29494.4
1.55-1.617.0190.2058.358698613067123930.9880.22194.8
1.61-1.697.2060.16610.348528312427118350.9920.17995.2
1.69-1.787.0640.12912.778019411876113530.9950.1495.6
1.78-1.897.230.10316.337748911160107180.9950.11196
1.89-2.026.920.08219.947070510572102180.9960.08996.7
2.02-2.197.0470.06823.6966918979294960.9970.07497
2.19-2.397.2240.06127.563445902487820.9980.06697.3
2.39-2.687.0750.05729.4455821809478900.9970.06297.5
2.68-3.096.6210.05131.0446935722470890.9980.05698.1
3.09-3.797.0580.04635.3341874602659330.9980.0598.5
3.79-5.356.7860.04135.9331587470146550.9990.04599
5.35-37.757.0530.0436.8317979257525490.9980.04499

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.2→37.75 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 10590 5 %
Rwork0.1477 201228 -
obs0.1485 211818 92.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88 Å2 / Biso mean: 23.0476 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.2→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 110 978 6644
Biso mean--17.29 34.79 -
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 (%)
1.2-1.210.33522340.32924452468662
1.21-1.220.32413090.29825862617180
1.22-1.240.28253210.27936117643886
1.24-1.260.28033320.27686319665186
1.26-1.270.2623320.25056304663688
1.27-1.290.25673460.2346568691490
1.29-1.310.24133450.22236547689290
1.31-1.330.24383530.21336696704993
1.33-1.350.21383510.20246706705792
1.35-1.370.24023530.18676711706493
1.37-1.390.19513590.18346788714794
1.39-1.420.2093580.17036817717594
1.42-1.450.18743560.16066752710893
1.45-1.480.18563590.15166831719094
1.48-1.510.16323590.14116823718294
1.51-1.540.16843590.13816826718594
1.54-1.580.16183620.12996868723095
1.58-1.620.15833650.12936937730295
1.62-1.670.15453610.12956871723295
1.67-1.730.16123660.13326923728995
1.73-1.790.16813650.14166964732996
1.79-1.860.15913660.13796959732596
1.86-1.940.14773680.13196981734996
1.94-2.050.14943670.14066973734096
2.05-2.180.15673720.13897055742797
2.18-2.340.15983720.13917077744997
2.34-2.580.1533720.14137061743398
2.58-2.950.16773750.15317131750698
2.95-3.720.14863750.14747140751599
3.72-37.750.12963780.12547169754799

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