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- PDB-8eix: Cobalt(II)-substituted S48A Horse Liver Alcohol Dehydrogenase in ... -

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Basic information

Entry
Database: PDB / ID: 8eix
TitleCobalt(II)-substituted S48A 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: 2.46 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: Nat.Chem. / Year: 2023
Title: Enhanced active-site electric field accelerates enzyme catalysis.
Authors: Zheng, C. / Ji, Z. / Mathews, I.I. / Boxer, S.G.
History
DepositionSep 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)81,87910
Polymers80,0452
Non-polymers1,8348
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-53 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.270, 57.560, 68.250
Angle α, β, γ (deg.)72.320, 74.880, 71.600
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 40022.453 Da / Num. of mol.: 2 / Mutation: S48A
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

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Non-polymers , 5 types, 35 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


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


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: tert-butanol(12%-20%), 2mM NADH, 3.3mM N-cyclohexylformamide, 1mM cobalt(II) acetate in 50mM 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: Mar 4, 2022
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: 2.46→37.36 Å / Num. obs: 27150 / % possible obs: 98.1 % / Redundancy: 6.945 % / Biso Wilson estimate: 65.986 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.15 / Χ2: 0.839 / Net I/σ(I): 9.4 / Num. measured all: 188569 / Scaling rejects: 401
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
2.46-2.526.7891.9641.5213531203619930.6352.1397.9
2.52-2.597.3511.6861.9214341199819510.741.81397.6
2.59-2.677.2311.3852.3713978197019330.7521.49298.1
2.67-2.757.2090.9893.2313271187718410.8671.06698.1
2.75-2.847.1470.8233.7812743183117830.9020.88797.4
2.84-2.947.0280.6194.7412003174617080.9350.66997.8
2.94-3.056.5970.4515.6611017170116700.9530.4998.2
3.05-3.186.9810.3077.6611268164816140.9780.33297.9
3.18-3.326.9070.2368.9310858159615720.9850.25598.5
3.32-3.487.2310.18710.9610709149914810.9880.20298.8
3.48-3.677.1220.15112.919843140213820.990.16398.6
3.67-3.897.010.11614.589436136813460.9920.12598.4
3.89-4.166.710.09915.758294126112360.9940.10798
4.16-4.496.1120.08316.777139119111680.9950.09198.1
4.49-4.926.3340.07719.186815108910760.9960.08498.8
4.92-5.57.0060.07919.668599929790.9950.08698.7
5.5-6.357.0320.08120.0459428708450.9930.08897.1
6.35-7.786.7070.06921.9547897267140.9950.07598.3
7.78-116.3260.05924.4235745775650.9970.06497.9
11-37.367.3690.06328.0521593082930.9980.06795.1

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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: 7RM6

7rm6


Resolution: 2.46→37.36 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 1367 5.04 %
Rwork0.206 25776 -
obs0.2079 27143 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.11 Å2 / Biso mean: 66.1779 Å2 / Biso min: 27.54 Å2
Refinement stepCycle: final / Resolution: 2.46→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 110 27 5705
Biso mean--60.16 59.43 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.550.38731380.35842584272298
2.55-2.650.35161380.31562543268198
2.65-2.770.30631320.29382592272498
2.77-2.920.33611370.28232556269398
2.92-3.10.31961420.26452578272098
3.1-3.340.29881370.24732580271799
3.34-3.670.26281360.21762584272099
3.67-4.20.23591360.19072594273098
4.2-5.30.18261360.16272580271699
5.3-37.360.18131350.15242585272098

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