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- PDB-1mg5: Crystal structure of Drosophila melanogaster alcohol dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 1mg5
TitleCrystal structure of Drosophila melanogaster alcohol dehydrogenase complexed with NADH and acetate at 1.6 A
Componentsalcohol dehydrogenase
KeywordsOXIDOREDUCTASE / SDR / ADH / Drosophila melanogaster / NADH / acetate
Function / homology
Function and homology information


acetyl-CoA biosynthetic process from ethanol / alcohol catabolic process / acetaldehyde metabolic process / ethanol metabolic process / alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / behavioral response to ethanol / alcohol dehydrogenase / aldehyde dehydrogenase (NAD+) activity / : ...acetyl-CoA biosynthetic process from ethanol / alcohol catabolic process / acetaldehyde metabolic process / ethanol metabolic process / alcohol metabolic process / alcohol dehydrogenase (NAD+) activity / behavioral response to ethanol / alcohol dehydrogenase / aldehyde dehydrogenase (NAD+) activity / : / protein homodimerization activity / cytosol
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
ACETATE ION / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBenach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Drosophila alcohol dehydrogenase: acetate-enzyme interactions and novel insights into the effects of electrostatics on catalysis
Authors: Benach, J. / Winberg, J.O. / Svendsen, J.S. / 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.
#2: 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.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: 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
Remark 999sequence Since the protein was purified directly from Drosophila melanogaster ADH. The first ...sequence Since the protein was purified directly from Drosophila melanogaster ADH. The first residue: Met1 is cleaved off in the matured Drosophila melanogaster ADH-S enzyme. For this reason it is not present in the crystal structure.

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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)56,7636
Polymers55,3142
Non-polymers1,4494
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-54 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.481, 69.519, 75.923
Angle α, β, γ (deg.)90.00, 89.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alcohol dehydrogenase


Mass: 27656.834 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ADH-Slow allele / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P00334, alcohol dehydrogenase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS/HCl, 30% PEG4000, 0.2M NaAcetate trihydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 8.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH8.6
310 mMdithiothreitol1reservoir
410 mMNADH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→40 Å / Num. obs: 60633 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 19.7
Reflection shellResolution: 1.63→1.68 Å / Rmerge(I) obs: 0.36 / % possible all: 73.3
Reflection
*PLUS
Num. measured all: 438968
Reflection shell
*PLUS
% possible obs: 73.3 % / Rmerge(I) obs: 0.36

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a4u

1a4u


Resolution: 1.63→20 Å / Isotropic thermal model: isotropic / Cross valid method: free R-factor / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.205 2894 5 %
Rwork0.168 --
all-61653 -
obs-61653 -
Displacement parametersBiso mean: 14.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3906 0 96 822 4824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.1
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.14
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.91

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