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- PDB-1deh: CRYSTALLIZATION OF HUMAN BETA1 ALCOHOL DEHYDROGENASE (15 MG/ML) I... -

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Basic information

Entry
Database: PDB / ID: 1deh
TitleCRYSTALLIZATION OF HUMAN BETA1 ALCOHOL DEHYDROGENASE (15 MG/ML) IN 50 MM SODIUM PHOSPHATE (PH 7.5), 2.0 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 OC, 13% (W/V) PEG 8000
ComponentsHUMAN BETA1 ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD+ DEPENDENT ALCOHOL DEHYDROGENASE
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 / ciliary basal body / cilium / 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 / ciliary basal body / cilium / 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 / 4-IODOPYRAZOLE / All-trans-retinol dehydrogenase [NAD(+)] ADH1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHurley, T.D. / Davis, G.J.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: X-ray structure of human beta3beta3 alcohol dehydrogenase. The contribution of ionic interactions to coenzyme binding.
Authors: Davis, G.J. / Bosron, W.F. / Stone, C.L. / Owusu-Dekyi, K. / Hurley, T.D.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Structure of Three Human Beta Alcohol Dehydrogenase Variants: Correlation with Their Functional Properties
Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M.
History
DepositionOct 14, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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: HUMAN BETA1 ALCOHOL DEHYDROGENASE
B: HUMAN BETA1 ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,55811
Polymers79,5472
Non-polymers2,0129
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-121 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.040, 44.540, 93.320
Angle α, β, γ (deg.)92.56, 103.26, 68.84
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 62 / 2: CIS PROLINE - PRO B 62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0776, 0.9799, -0.1838), (0.9784, -0.1103, -0.1748), (-0.1915, -0.1662, -0.9673)
Vector: -10.124, -6.309, -91.017)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HUMAN BETA1 ALCOHOL DEHYDROGENASE / BETA1 ADH


Mass: 39773.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE STRUCTURE FOR HOMODIMERIC BETA1 ALCOHOL DEHYDROGENASE WAS SOLVED WITH ONE NAD+ AND ONE 4-IODOPYRAZOLE PER SUBUNIT
Source: (gene. exp.) Homo sapiens (human)
Description: ADH2 - STANDARD CONVENTION IS TO DENOTE THE POLYMORPHISM WITH A 1 IN SUPERSCRIPT, I.E., ADH2==1==)
Gene: HUMAN BETA1 CDNA / Organ: LIVER / Plasmid: PKK223-3 / Gene (production host): HUMAN BETA1 CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P00325, alcohol dehydrogenase

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Non-polymers , 5 types, 323 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-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3IN2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMsodium phosphate1reservoir
32 mMNAD+1reservoir
41 mM4-iodopyrazole1reservoir
513.5 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1995 / Details: 03-27
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.19→46 Å / Num. obs: 34095 / % possible obs: 83 % / Observed criterion σ(I): 0.5 / Redundancy: 2 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Num. measured all: 67571 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 70 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
R-AXISIIC (HAGASHI/RIGAKU)data reduction
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.261 -7 %
Rwork0.18 --
obs0.18 32940 84 %
Displacement parametersBiso mean: 29.55 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 105 314 5981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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