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- PDB-1b16: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1b16
TitleALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-3-PENTANONE
ComponentsPROTEIN (ALCOHOL DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES / TERNARY COMPLEX / NAD-3- PENTANONE 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
Chem-NAQ / Alcohol dehydrogenase
Similarity search - Component
Biological speciesScaptodrosophila lebanonensis (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: BNL / Processing site: RCSB
Revision 1.0Nov 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: PROTEIN (ALCOHOL DEHYDROGENASE)
B: PROTEIN (ALCOHOL DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1434
Polymers55,6482
Non-polymers1,4952
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-46 kcal/mol
Surface area18280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.800, 53.000, 70.500
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.983274, -0.169734, 0.066045), (-0.169547, 0.720587, -0.672316), (0.066524, -0.672268, -0.737312)
Vector: 23.22419, 12.3101, 25.47263)

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Components

#1: Protein PROTEIN (ALCOHOL DEHYDROGENASE) / E.C.1.1.1.1 OXIDOREDUCTASE


Mass: 27823.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NAD-3-PENTANONE / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase
#2: Chemical ChemComp-NAQ / NICOTINAMIDE ADENINE DINUCLEOTIDE 3-PENTANONE ADDUCT


Mass: 747.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H35N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNAD-3-PENTANONE ADDUCT

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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% 3-PENTANONE, 4 C.
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.6 / Method: vapor diffusion, sitting drop
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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9511
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9511 Å / Relative weight: 1
ReflectionResolution: 1.32→15 Å / Num. obs: 103695 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 3
Reflection shellResolution: 1.32→1.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 94
Reflection
*PLUS
Num. measured all: 262892
Reflection shell
*PLUS
% possible obs: 94 %

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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: 1.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.17
RfactorNum. reflection% reflection
Rfree0.213 -5 %
Rwork0.184 --
obs-84601 -
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 100 485 4511
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_deg1.89
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.55
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.92

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