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- PDB-8ecu: F93S Horse Liver Alcohol Dehydrogenase in Complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 8ecu
TitleF93S 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: 1.3 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 F93S horse liver alcohol dehydrogenase at 1.30 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)81,80410
Polymers79,9572
Non-polymers1,8478
Water16,033890
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-112 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.030, 49.770, 92.570
Angle α, β, γ (deg.)93.270, 102.800, 108.490
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39978.355 Da / Num. of mol.: 2 / Mutation: F93S
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.: 890 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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: 1.3→39.27 Å / Num. obs: 164848 / % possible obs: 93 % / Redundancy: 9.605 % / Biso Wilson estimate: 22.114 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.104 / Χ2: 0.855 / Net I/σ(I): 10.75 / Num. measured all: 1583338 / Scaling rejects: 812
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
1.3-1.337.5411.281.478584213139113830.7641.37386.6
1.33-1.377.6341.031.868353312765109420.8481.10485.7
1.37-1.417.6310.852.227725312418101240.890.91181.5
1.41-1.457.7460.6942.788375912084108130.9160.74389.5
1.45-1.57.8280.5543.438149311695104110.9440.59389
1.5-1.5510.6970.544.511491411342107430.9610.56794.7
1.55-1.6110.3290.4215.5210693210902103530.9670.44395
1.61-1.6810.4120.3336.6510414410471100020.9790.35195.5
1.68-1.7510.9310.2658.411056411009096640.9880.27895.8
1.75-1.8410.7620.20810.5399849968692780.9910.21895.8
1.84-1.9410.5190.1613.0892638911788070.9940.16996.6
1.94-2.0610.2050.13315.2185376865883660.9950.1496.6
2.06-2.210.7710.11318.8285450817079330.9960.11997.1
2.2-2.3710.6090.09921.3278218755173730.9960.10497.6
2.37-2.610.6660.09322.8673020699468460.9970.09897.9
2.6-2.9110.1390.08324.0262355628361500.9960.08797.9
2.91-3.3610.3310.07626.7856438553154630.9970.0898.8
3.36-4.1110.5550.07129.0248861469646290.9970.07498.6
4.11-5.8110.0320.06528.5635983361735870.9980.06899.2
5.81-39.2710.9230.06830.5121639199819810.9980.07199.1

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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: 1.3→39.27 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1644 8241 5 %
Rwork0.1419 156535 -
obs0.143 164776 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.25 Å2 / Biso mean: 23.7768 Å2 / Biso min: 11.93 Å2
Refinement stepCycle: final / Resolution: 1.3→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5560 0 110 890 6560
Biso mean--18.32 36.93 -
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 (%)
1.3-1.310.32412570.28364878513586
1.31-1.330.31192550.2674837509287
1.33-1.350.29632560.25044857511386
1.35-1.360.28292500.23424763501386
1.36-1.380.27552510.22834748499984
1.38-1.40.25552270.22344317454478
1.4-1.420.25792650.20975038530388
1.42-1.440.26422610.19964947520890
1.44-1.460.22252650.17865041530689
1.46-1.490.21062610.16494956521789
1.49-1.510.19342730.15565179545292
1.51-1.540.19232770.14475251552895
1.54-1.570.18552830.13535381566495
1.57-1.60.17222780.13045282556095
1.6-1.640.1822800.12745319559995
1.64-1.680.15932830.12275366564996
1.68-1.720.16762850.12055416570196
1.72-1.760.14312850.1195418570396
1.76-1.820.16652790.12785320559996
1.82-1.870.15572810.13275349563096
1.87-1.940.16762890.13045467575697
1.94-2.020.15842830.13265403568696
2.02-2.110.15882880.12795473576197
2.11-2.220.15682860.13345421570797
2.22-2.360.15512880.13245475576398
2.36-2.540.15032880.13675491577998
2.54-2.80.16282910.14785510580198
2.8-3.210.16972910.15295527581898
3.21-4.040.14612920.13655544583699
4.04-39.270.13122930.12545561585499

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