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- PDB-1htb: CRYSTALLIZATION OF HUMAN BETA3 ALCOHOL DEHYDROGENASE (10 MG/ML) I... -

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Basic information

Entry
Database: PDB / ID: 1htb
TitleCRYSTALLIZATION OF HUMAN BETA3 ALCOHOL DEHYDROGENASE (10 MG/ML) IN 100 MM SODIUM PHOSPHATE (PH 7.5), 7.5 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 C
ComponentsBETA3 ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD+ DEPENDENT ALCOHOL DEHYDROGENASE
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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, zinc-dependent / : / 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 / 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: 2.4 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
Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M.
History
DepositionAug 10, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: 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: BETA3 ALCOHOL DEHYDROGENASE
B: BETA3 ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,45011
Polymers79,4382
Non-polymers2,0129
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-128 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.030, 44.430, 92.740
Angle α, β, γ (deg.)92.71, 103.17, 69.15
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: (0.0737, 0.9799, -0.1853), (0.9784, -0.1071, -0.1768), (-0.193, -0.1683, -0.9667)
Vector: -10.218, -6.415, -90.967)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA3 ALCOHOL DEHYDROGENASE / BETA3 ADH


Mass: 39719.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HOMODIMERIC WITH ONE NAD+ AND ONE 4-IODOPYRAZOLE PER SUBUNIT
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN BETA3 CDNA / Organ: LIVER / Plasmid: PKK223-3 / Gene (production host): HUMAN BETA3 CDNA / Production host: Escherichia coli (E. coli) / References: UniProt: P00325, alcohol dehydrogenase

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Non-polymers , 5 types, 151 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 / 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlrecombinant human beta31drop
2100 mMsodium phosphate1drop
37.5 mMNAD+1drop
41 mM4-iodopyrazole1drop
516.5 %(w/v)PEG80001drop

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→47.97 Å / Num. obs: 26989 / % possible obs: 83.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 53103 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.51 Å / % possible obs: 70 %

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Processing

Software
NameVersionClassification
RAXISIIC DATA PROCESSING SOFTWARE T. HAGASHIdata collection
RIGAKUCORPORATIONdata collection
JAPANdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISIIC (HAGASHI/RIGAKU)data reduction
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 1
Details: THE FOLLOWING DISTANCES ARE SIMILAR TO THOSE FOUND IN 1HDY (REFERENCE 1 ABOVE) AND ARE ALSO SIMILAR TO THE INTERACTION DISTANCES REPORTED BY EKLUND, H., SAMAMA, J.-P., WALLEN, L. (1982) ...Details: THE FOLLOWING DISTANCES ARE SIMILAR TO THOSE FOUND IN 1HDY (REFERENCE 1 ABOVE) AND ARE ALSO SIMILAR TO THE INTERACTION DISTANCES REPORTED BY EKLUND, H., SAMAMA, J.-P., WALLEN, L. (1982) PYRAZOLE BINDING IN CRYSTALLINE BINARY AND TERNARY COMPLEXES WITH LIVER ALCOHOL DEHYDROGENASE. BIOCHEMISTRY, VOL. 21, PP. 4858 - 4866) BETWEEN 4-IODOPYRAZOLE AND HORSE LIVER EE ADH (NO PDB ENTRY). SIMILAR CONTACT DISTANCES ARE ALSO FOUND IN 1DEH. 4-IODOPYRAZOLE FORMS A TRANSITION-STATE-LIKE COMPLEX WITH ADH AND EXHIBITS NEARLY COVALENT BOND CONTACT DISTANCES BETWEEN ITS TWO ADJACENT NITROGENS AND THE C4 ATOM OF NAD+ AND THE CATALYTIC ZINC ATOM: 377 A NAD NC4 378 A PYZ N2 HET-HET 1.7 376 B ZN ZN 378 B PYZ N1 HET-HET 2.0 377 B NAD NC4 378 B PYZ N2 HET-HET 2.1 376 A ZN ZN 378 A PYZ N1 HET-HET 2.3 RESIDUE ILE 368 IS AN OUTLIER IN THE RAMACHANDRAN PLOT. IT LIES IN THIS REGION OF THE RAMACHANDRAN PLOT IN ALL ADH STRUCTURES DEPOSITED IN THE DATA BANK. THUS, IT APPEARS THAT LOCAL STRUCTURAL FEATURES CONSTRAIN ITS CONFORMATION TO THIS POSITION. SER B 298 APPEARS TO OCCUPY AT LEAST TWO DISTINCT CONFORMATIONS. THE AUTHORS HAVE NOT ATTEMPTED TO MODEL POSITIONAL DISORDER, BUT ANY ONE CONFORMATION DOES NOT REFINE WELL TO THE OBSERVED DENSITY. THIS PROBLEM DOES NOT OCCUR IN THE A SUBUNIT.
RfactorNum. reflection% reflection
Rfree0.243 -7 %
Rwork0.175 --
obs0.175 25643 85.9 %
Displacement parametersBiso mean: 24.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 105 142 5799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
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
Highest resolution: 2.4 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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