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- PDB-1b15: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1b15
TitleALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-ACETONE
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / TERNARY COMPLEX / NAD- ACETONE ADDUCT
Function / homology
Function and homology information


alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / identical protein binding / cytoplasm
Similarity search - Function
Alcohol dehydrogenase, Drosophila-type / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT / Alcohol dehydrogenase
Similarity search - Component
Biological speciesScaptodrosophila lebanonensis (fry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBenach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 A resolution by X-ray crystallography.
Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The Refined Crystal Structure of Drosophila Lebanonensis Alcohol Dehydrogenase at 1.9 A Resolution
Authors: Benach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
History
DepositionNov 25, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0874
Polymers55,6482
Non-polymers1,4392
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-45 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.700, 53.500, 70.700
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.982541, -0.172445, 0.06983), (-0.173803, 0.716854, -0.675213), (0.066379, -0.675561, -0.73431)
Vector: 23.21279, 12.30627, 25.42021)

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 27823.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NAD-ACETONE / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase
#2: Chemical ChemComp-NAE / NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT


Mass: 719.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.15 Å3/Da / Density % sol: 45.5 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 28% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH=7.5, 1MM NAD+, 1% ACETONE, 277 K.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.6 / Method: vapor diffusion, sitting drop / Details: Ladenstein, R., (1995) Acta Crystallog., D51, 69.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1drop
31 %isopropanol1drop
42 mMdithiothreitol1drop
528 %PEG20001reservoir
60.2 M1reservoirCaCl2
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. obs: 25664 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.27 / % possible all: 100
Reflection
*PLUS
Num. measured all: 108862
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
X-PLORmodel building
REFMACrefinement
AMoREphasing
CCP4model building
Omodel building
MAINmodel building
RAVEmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CCP4phasing
MAINphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A4U

1a4u


Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -10 %
Rwork0.198 --
obs-22665 -
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 96 130 4150
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_deg2.2
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24.43
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg2.11

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