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- PDB-1b2l: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS: TERNARY COMPL... -

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Basic information

Entry
Database: PDB / ID: 1b2l
TitleALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS: TERNARY COMPLEX WITH NAD-CYCLOHEXANONE
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / TERNARY COMPLEX / NAD- CYCLOHEXANONE 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
CYCLOHEXANONE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / NICOTINAMIDE ADENINE DINUCLEOTIDE CYCLOHEXANONE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesScaptodrosophila lebanonensis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 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: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8765
Polymers27,8241
Non-polymers1,0524
Water4,179232
1
A: ALCOHOL DEHYDROGENASE
hetero molecules

A: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,75210
Polymers55,6482
Non-polymers2,1048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area8700 Å2
ΔGint-58 kcal/mol
Surface area18180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.100, 54.100, 168.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

CA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALCOHOL DEHYDROGENASE /


Mass: 27823.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CYCLOHEXANONE / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NDC / NICOTINAMIDE ADENINE DINUCLEOTIDE CYCLOHEXANONE


Mass: 759.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N7O15P2
#4: Chemical ChemComp-CYH / CYCLOHEXANONE / Cyclohexanone


Mass: 98.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 277 K / pH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH= 8.0, 1MM NAD+, 1% CYCLOHEXANONE, 277 K.
Crystal grow
*PLUS
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. obs: 40649 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 3
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 3 / % possible all: 91
Reflection
*PLUS
Num. measured all: 565296
Reflection shell
*PLUS
% possible obs: 91 %

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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: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.18
RfactorNum. reflection% reflection
Rfree0.212 -5 %
Rwork0.19 --
obs-38275 -
Displacement parametersBiso mean: 11.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 67 232 2262
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_deg1.85
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.7
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.94

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