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- PDB-5vjg: horse liver alcohol dehydrogenase complexed with 2,2'bipyridine -

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Basic information

Entry
Database: PDB / ID: 5vjg
Titlehorse liver alcohol dehydrogenase complexed with 2,2'bipyridine
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / 2 / 2'bipyridine / horse liver / zinc chelation
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. / 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
2,2'-bipyridine / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPlapp, B.V. / Baskar Raj, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
#1: Journal: Eur. J. Biochem. / Year: 1977
Title: X-ray investigation of the binding of 1,10-phenanthroline and imidazole to horse-liver alcohol dehydrogenase.
Authors: Boiwe, T. / Branden, C.I.
#2: Journal: J. Mol. Biol. / Year: 1976
Title: Three-dimensional structure of horse liver alcohol dehydrogenase at 2-4 A resolution.
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1404
Polymers39,8531
Non-polymers2873
Water1,72996
1
A: Alcohol dehydrogenase E chain
hetero molecules

A: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2818
Polymers79,7072
Non-polymers5746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3310 Å2
ΔGint-21 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 73.700, 181.140
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 E chain


Mass: 39853.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0BP / 2,2'-bipyridine


Mass: 156.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: Dialysis of 10 mg protein/ml against 50 mM Tris-HCl, pH 8.4, as the concentration of 2-methyl-2,4-pentanediol concentration was raised to 25 %. Crysta was soaked for 3 hr iwth 30 mM 2,2'- ...Details: Dialysis of 10 mg protein/ml against 50 mM Tris-HCl, pH 8.4, as the concentration of 2-methyl-2,4-pentanediol concentration was raised to 25 %. Crysta was soaked for 3 hr iwth 30 mM 2,2'-bipyridine before flash vitrification with liquid N2.l

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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 23, 2005 / 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: 1.9→20 Å / Num. obs: 27148 / % possible obs: 95.3 % / Redundancy: 6.99 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.118 / Χ2: 0.96 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.04 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2560 / Χ2: 0.83 / % possible all: 87.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREKdata reduction
d*TREKdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
Omodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ADH

8adh


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.554 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 1174 4.1 %RANDOM
Rwork0.2044 ---
obs0.2075 27148 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.23 Å2 / Biso mean: 41.412 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-0 Å2
2--0.91 Å20 Å2
3----3.33 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 14 96 2895
Biso mean--47.63 40.78 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192850
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.983852
X-RAY DIFFRACTIONr_angle_other_deg1.04336485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.961512
X-RAY DIFFRACTIONr_chiral_restr0.10.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213177
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02587
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.462 82 4.7 %
Rwork0.378 1739 -
obs--85.69 %

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