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- PDB-1oof: Complex of Drosophila odorant binding protein LUSH with ethanol -

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Basic information

Entry
Database: PDB / ID: 1oof
TitleComplex of Drosophila odorant binding protein LUSH with ethanol
Componentsodorant binding protein LUSH
KeywordsTRANSPORT PROTEIN / LUSH / Alcohol / Odorant Binding
Function / homology
Function and homology information


diphenyl phthalate binding / dibutyl phthalate binding / courtship behavior / olfactory behavior / response to pheromone / pheromone binding / odorant binding / sensory perception of smell / response to ethanol / extracellular region
Similarity search - Function
Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / ETHANOL / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.49 Å
AuthorsKruse, S.W. / Zhao, R. / Smith, D.P. / Jones, D.N.M.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of a specific alcohol-binding site defined by the odorant binding protein LUSH from Drosophila melanogaster
Authors: Kruse, S.W. / Zhao, R. / Smith, D.P. / Jones, D.N.M.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: odorant binding protein LUSH
B: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7598
Polymers28,4312
Non-polymers3286
Water4,216234
1
A: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3804
Polymers14,2161
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3804
Polymers14,2161
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.942, 46.942, 111.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein odorant binding protein LUSH


Mass: 14215.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Oregon R / Tissue: subset of trichoid olfactory sensilla / Gene: lush / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O02372
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, ethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 or 18 ℃ / pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium acetate1reservoirpH4.0
225-30 %(w/v)PEG40001reservoir
30.3 %(v/v)alcohol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97895 Å
DetectorType: SBC-1 / Detector: CCD / Date: Feb 21, 2002 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. all: 39458 / Num. obs: 38748 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 25.4
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3918 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 119487
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.49→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.155 / SU ML: 0.081 / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21002 3785 10 %RANDOM
Rwork0.17821 ---
all0.18135 35363 --
obs0.18135 33970 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 16 240 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222094
X-RAY DIFFRACTIONr_bond_other_d0.0020.021892
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9762804
X-RAY DIFFRACTIONr_angle_other_deg1.03634460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4813246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.82315441
X-RAY DIFFRACTIONr_chiral_restr0.0830.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022244
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02400
X-RAY DIFFRACTIONr_nbd_refined0.2320.3481
X-RAY DIFFRACTIONr_nbd_other0.1920.31741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.5151
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.525
X-RAY DIFFRACTIONr_mcbond_it1.031.51272
X-RAY DIFFRACTIONr_mcangle_it1.83222056
X-RAY DIFFRACTIONr_scbond_it3.0153822
X-RAY DIFFRACTIONr_scangle_it4.9784.5748
LS refinement shellResolution: 1.49→1.57 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.239 569
Rwork0.201 4766
obs-5330
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.445

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