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- PDB-6cy3: Horse liver E267N alcohol dehydrogenase complex with 3'-dephospho... -

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Basic information

Entry
Database: PDB / ID: 6cy3
TitleHorse liver E267N alcohol dehydrogenase complex with 3'-dephosphocoenzyme A
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / NAD-dependent horse liver alcohol dehydrogenase E267N mutant 3'-dephosphocoenzyme A
Function / homology
Function and homology information


alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / NAD-retinol dehydrogenase 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. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DEPHOSPHO COENZYME A / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPlapp, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AA00279 United States
CitationJournal: Arch. Biochem. Biophys. / Year: 2018
Title: Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A.
Authors: Kim, Y.H. / Gogerty, D.S. / Plapp, B.V.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)40,6574
Polymers39,8381
Non-polymers8183
Water82946
1
A: alcohol dehydrogenase
hetero molecules

A: alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3138
Polymers79,6772
Non-polymers1,6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6430 Å2
ΔGint-137 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 74.010, 182.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein alcohol dehydrogenase /


Mass: 39838.262 Da / Num. of mol.: 1 / Mutation: E267N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EQUUS CABALLUS (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: needles
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: 10 mtg/ml enzyme dialyzed against 50 mM tris(hydroxymethyl)aminomethane-HCl, 0.25 mM EDTA, containing 2-methy-2,4-pentanediol increasing to 25 %.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2004 / Details: MSC YALE CONFOCAL OSMIC
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 14923 / % possible obs: 87.1 % / Redundancy: 4.97 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.042 / Rrim(I) all: 0.091 / Χ2: 1.18 / Net I/av σ(I): 12.4 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.385.50.2534.615680.790.1190.2760.8993.9
2.38-2.485.460.2075.415650.2260.992.8
2.48-2.595.440.1886.115730.2060.9592.9
2.59-2.735.310.1487.715590.1611.0191.4
2.73-2.95.160.1279.115390.1391.191.3
2.9-3.124.910.11511.315060.1261.2889
3.12-3.434.550.08715.814670.0961.486.5
3.43-3.934.740.11115.314940.1241.6386.2
3.93-4.934.270.05726.412530.0641.5772.1
4.93-19.964.070.03935.813990.0441.4676.4

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qlh
Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.677 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.359
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3101 1499 10.1 %RANDOM
Rwork0.2219 ---
obs0.2308 13389 86.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.33 Å2 / Biso mean: 53.912 Å2 / Biso min: 28.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0 Å2-0 Å2
2--7.73 Å20 Å2
3----7.2 Å2
Refinement stepCycle: final / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 46 46 2876
Biso mean--59.81 44.37 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192882
X-RAY DIFFRACTIONr_bond_other_d0.0020.022774
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9923902
X-RAY DIFFRACTIONr_angle_other_deg0.99436456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0495373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81624.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39415497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3621512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213154
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02543
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 117 -
Rwork0.364 1017 -
all-1134 -
obs--93.95 %

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