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- PDB-1a4u: ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS -

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Basic information

Entry
Database: PDB / ID: 1a4u
TitleALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DETOXIFICATION / METABOLISM / ALCOHOL DEHYDROGENASE / DROSOPHILA LEBANONENSIS / SHORT-CHAIN DEHYDROGENASES/REDUCTASES
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
Alcohol dehydrogenase
Similarity search - Component
Biological speciesScaptodrosophila lebanonensis (fry)
MethodX-RAY DIFFRACTION / molecular replacement, SIR / Resolution: 1.92 Å
AuthorsBenach, J. / Atrian, S. / Gonzalez-Duarte, R. / Ladenstein, R.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Well Ordered Crystals of a Short-Chain Alcohol Dehydrogenase from Drosophila Lebanonensis: Re-Evaluation of the Crystallographic Data and Rotation-Function Analysis
Authors: Ladenstein, R. / Tibbelin, G. / Karshikoff, A. / Atrian, S. / Gonzalez-Duarte, R.
History
DepositionFeb 5, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)55,6482
Polymers55,6482
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-38 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.495, 55.599, 70.070
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.983038, -0.171218, 0.065733), (-0.170017, 0.716338, -0.676723), (0.06878, -0.67642, -0.733297)
Vector: 22.28401, 12.12351, 25.31697)

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 27823.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Scaptodrosophila lebanonensis (fry) / References: UniProt: P10807, alcohol dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.3 mg/mlprotein1drop
224 %(w/v)PEG20001reservoir
30.2 M1reservoirCaCl2
40.1 MTris-HCl1reservoir
52 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→25 Å / Num. obs: 36568 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 1.92→1.98 Å / Rmerge(I) obs: 0.386 / % possible all: 87
Reflection
*PLUS
Num. measured all: 124898
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameClassification
MAINmodel building
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
MAINphasing
X-PLORphasing
RefinementMethod to determine structure: molecular replacement, SIR
Starting model: 2HSD

2hsd


Resolution: 1.92→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: X-PLOR 3.1 AND 3.851 WERE USED RESIDUES FROM 186-191 HAVE CRYSTALLOGRAPHIC WEIGHT ZERO.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3551 10 %RANDOM
Rwork0.205 ---
obs0.205 35479 97.45 %-
Displacement parametersBiso mean: 22.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.92→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 0 165 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg1.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.56
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.9221.5
X-RAY DIFFRACTIONx_mcangle_it4.612
X-RAY DIFFRACTIONx_scbond_it2.9932
X-RAY DIFFRACTIONx_scangle_it3.6252.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDWeight Biso Weight position
11X-RAY DIFFRACTION1300
22X-RAY DIFFRACTION1.5250
LS refinement shellResolution: 1.92→2.01 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2778 430 10 %
Rwork0.2041 3805 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAMTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.56
LS refinement shell
*PLUS
Rfactor obs: 0.2041

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