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- PDB-1u3u: Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Is... -

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Basic information

Entry
Database: PDB / ID: 1u3u
TitleCrystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution
ComponentsAlcohol dehydrogenase beta chain
KeywordsOXIDOREDUCTASE
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 / zinc ion binding / nucleoplasm ...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 / 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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
N-BENZYLFORMAMIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / All-trans-retinol dehydrogenase [NAD(+)] ADH1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGibbons, B.J. / Hurley, T.D.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of three class I human alcohol dehydrogenases complexed with isoenzyme specific formamide inhibitors
Authors: Gibbons, B.J. / Hurley, T.D.
History
DepositionJul 23, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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_asym_id / _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_asym_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: Alcohol dehydrogenase beta chain
B: Alcohol dehydrogenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,50011
Polymers79,5472
Non-polymers1,9549
Water20,6631147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-130 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.080, 52.510, 90.120
Angle α, β, γ (deg.)79.76, 89.67, 68.97
Int Tables number1
Space group name H-MP1
DetailsThe assymetric unit contains one homodimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase beta chain / Alcohol Dehydrogenase Beta-1-Beta-1 Isoform


Mass: 39773.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH1B / Plasmid: pKK2233 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P00325, alcohol dehydrogenase

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Non-polymers , 5 types, 1156 molecules

#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-BNF / N-BENZYLFORMAMIDE


Mass: 135.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1147 / 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: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15mg/ml enzyme, 2mM NAD+, 50mM sodium phosphate, and 11.5-13% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54059 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54059 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 88679 / Num. obs: 88679 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 6.6 / Num. unique all: 8039 / % possible all: 82.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HSZ

1hsz


Resolution: 1.6→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4471 -random
Rwork0.169 ---
all0.17 88679 --
obs0.17 88679 90.7 %-
Displacement parametersBiso mean: 14.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 117 1147 6826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.23
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d25.16
X-RAY DIFFRACTIONc_improper_angle_d1.46

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