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- PDB-5vkr: Horse liver alcohol dehydrogenase complexed with adenosine-5-diph... -

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Basic information

Entry
Database: PDB / ID: 5vkr
TitleHorse liver alcohol dehydrogenase complexed with adenosine-5-diphosphoribose
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / horse liver / ADPR / adenosine-5-diphosphoribose / zinc
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
ADENOSINE-5-DIPHOSPHORIBOSE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPlapp, B.V. / Rubach, J.K. / Ramaswamy, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08365 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: 1975
Title: The conformation of adenosine diphosphoribose and 8-bromoadenosine diphosphoribose when bound to liver alcohol dehydrogenase.
Authors: Abdallah, M.A. / Biellmann, J.F. / Nordstrom, B. / 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 22, 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)40,5434
Polymers39,8531
Non-polymers6903
Water81145
1
A: Alcohol dehydrogenase E chain
hetero molecules

A: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0878
Polymers79,7072
Non-polymers1,3806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.370, 74.270, 180.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: needles
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: 10 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5- ...Details: 10 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5-diphosphoribose in the final outer dialysate for 1 hr. Crystal flash vitrified by plunging it into liquid N2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0093 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2001 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 30816 / % possible obs: 91.7 % / Redundancy: 7.64 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.117 / Χ2: 1.16 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.68 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2947 / Χ2: 1.23 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ADH

8adh


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.514 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24775 1328 4.1 %RANDOM
Rwork0.19001 ---
obs0.19233 30816 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0 Å2
2--3.2 Å20 Å2
3----3.37 Å2
Refinement stepCycle: 1 / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 38 45 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192876
X-RAY DIFFRACTIONr_bond_other_d0.0020.022809
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.993895
X-RAY DIFFRACTIONr_angle_other_deg1.08636510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31124.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8215498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8671512
X-RAY DIFFRACTIONr_chiral_restr0.1230.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02585
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1644.5421495
X-RAY DIFFRACTIONr_mcbond_other4.1134.5381494
X-RAY DIFFRACTIONr_mcangle_it5.5646.8061867
X-RAY DIFFRACTIONr_mcangle_other5.586.8081868
X-RAY DIFFRACTIONr_scbond_it6.4755.4391381
X-RAY DIFFRACTIONr_scbond_other6.4745.441382
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7987.7882029
X-RAY DIFFRACTIONr_long_range_B_refined11.4437.0073070
X-RAY DIFFRACTIONr_long_range_B_other11.43136.9953067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 76 -
Rwork0.371 2129 -
obs--85.56 %

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