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- PDB-1ooi: Crystal structure of LUSH from Drosophila melanogaster at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 1ooi
TitleCrystal structure of LUSH from Drosophila melanogaster at pH 6.5
Componentsodorant binding protein LUSH
KeywordsTRANSPORT PROTEIN / LUSH / Alcohol / Odorant-Binding Protein
Function / homology
Function and homology information


diphenyl phthalate binding / dibutyl phthalate binding / response to pheromone / courtship behavior / pheromone binding / olfactory behavior / 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
General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: odorant binding protein LUSH


Theoretical massNumber of molelcules
Total (without water)14,2161
Polymers14,2161
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.370, 55.370, 66.946
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein odorant binding protein LUSH


Mass: 14215.508 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, MOPS, n-butanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1droppH8.0
20.3 %(v/v)n-butanol1drop
3100 mMMOPS1reservoirpH6.5
430 %(w/v)PEG40001reservoir
50.3 %(v/v)n-butanol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 23, 2002 / Details: osmic blue optics
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. all: 7504 / Num. obs: 7504 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 57.9
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 10.7 / Num. unique all: 728 / % possible all: 100
Reflection
*PLUS
Num. measured all: 112114
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OOF

1oof


Resolution: 2.04→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24663 787 10.6 %RANDOM
Rwork0.19537 ---
all0.20083 6675 --
obs0.20083 6634 99.38 %-
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: 27.792 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.04→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 0 90 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221010
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9721357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1973123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.32915204
X-RAY DIFFRACTIONr_chiral_restr0.080.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02756
X-RAY DIFFRACTIONr_nbd_refined0.2340.3509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.585
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.52
X-RAY DIFFRACTIONr_mcbond_it1.8431.5623
X-RAY DIFFRACTIONr_mcangle_it2.94921005
X-RAY DIFFRACTIONr_scbond_it5.333387
X-RAY DIFFRACTIONr_scangle_it7.7644.5352
LS refinement shellResolution: 2.04→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.271 103
Rwork0.215 478
obs-1054
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.172
LS refinement shell
*PLUS
Rfactor Rwork: 0.209

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