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- PDB-1hsz: HUMAN BETA-1 ALCOHOL DEHYDROGENASE (ADH1B*1) -

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Basic information

Entry
Database: PDB / ID: 1hsz
TitleHUMAN BETA-1 ALCOHOL DEHYDROGENASE (ADH1B*1)
ComponentsCLASS I ALCOHOL DEHYDROGENASE 1, BETA SUBUNIT
KeywordsOXIDOREDUCTASE / rossmann fold / alcohol dehydrogenase / zinc
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / all-trans-retinol dehydrogenase (NAD+) activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / cilium / ciliary basal body / zinc ion binding ...all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / all-trans-retinol dehydrogenase (NAD+) activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / cilium / ciliary basal body / zinc ion binding / nucleoplasm / plasma membrane / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / All-trans-retinol dehydrogenase [NAD(+)] ADH1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNiederhut, M.S. / Gibbons, B.J. / Perez-Miller, S. / Hurley, T.D.
CitationJournal: Protein Sci. / Year: 2001
Title: Three-dimensional structures of the three human class I alcohol dehydrogenases.
Authors: Niederhut, M.S. / Gibbons, B.J. / Perez-Miller, S. / Hurley, T.D.
History
DepositionDec 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLASS I ALCOHOL DEHYDROGENASE 1, BETA SUBUNIT
B: CLASS I ALCOHOL DEHYDROGENASE 1, BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2309
Polymers79,5472
Non-polymers1,6837
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-127 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.9, 53.4, 90.2
Angle α, β, γ (deg.)79.9, 89.5, 69.3
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Detailsbiological dimer is contained in the asymmetric unit

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Components

#1: Protein CLASS I ALCOHOL DEHYDROGENASE 1, BETA SUBUNIT / E.C.1.1.1.1 / ADH BETA-1-SUBUNIT / ALCOHOL DEHYDROGENASE 2 (CLASS I) / BETA POLYPEPTIDE


Mass: 39773.277 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH2 OR ADH1B*1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P00325, 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM sodium phosphate, 2 mM NAD+, 14% (w/v) PEG 8000, 14 mg/ml protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG800011
250 mMsodium phosphate11
32 mMNAD+11
414 mg/mlprotein11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 22, 1998 / Details: yale focusing mirrors
RadiationMonochromator: yale focusing mirrors with nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→44 Å / Num. all: 37772 / Num. obs: 33051 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.12 / % possible all: 64.5
Reflection
*PLUS
Num. measured all: 66027
Reflection shell
*PLUS
% possible obs: 64.5 % / Mean I/σ(I) obs: 7.4

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DEH

1deh


Resolution: 2.2→44 Å / Isotropic thermal model: isotropic individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2345 7.1 %random
Rwork0.193 ---
all0.194 37772 --
obs0.194 33051 --
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 97 514 6173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_improper_angle_d1.44

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