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- PDB-2gte: Drosophila OBP LUSH bound to attractant pheromone 11-cis-vaccenyl... -

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Basic information

Entry
Database: PDB / ID: 2gte
TitleDrosophila OBP LUSH bound to attractant pheromone 11-cis-vaccenyl acetate
ComponentsGeneral odorant-binding protein lush
KeywordsTRANSPORT PROTEIN / pheromone binding protein / odorant binding protein / pheromone
Function / homology
Function and homology information


diphenyl phthalate binding / courtship behavior / dibutyl phthalate binding / response to pheromone / 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
PHOSPHATE ION / (Z)-OCTADEC-11-ENYL ACETATE / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLaughlin, J.D. / Ha, T. / Smith, D.P. / Jones, D.N.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Activation of pheromone-sensitive neurons is mediated by conformational activation of pheromone-binding protein
Authors: Laughlin, J.D. / Ha, T.S. / Jones, D.N. / Smith, D.P.
History
DepositionApr 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General odorant-binding protein lush
B: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1475
Polymers28,4312
Non-polymers7163
Water7,494416
1
A: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6213
Polymers14,2161
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5262
Polymers14,2161
Non-polymers3111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.124, 65.270, 80.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein General odorant-binding protein lush


Mass: 14215.508 Da / Num. of mol.: 2 / Fragment: Residues 30-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lush / Plasmid: pET13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O02372
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-VA / (Z)-OCTADEC-11-ENYL ACETATE / Vaccenyl acetate


Mass: 310.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H38O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1:1 protein/well sol. (4ul total) over 0.5 mL well, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.127 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.4→41.2 Å / Num. obs: 55876 / % possible obs: 99.9 % / Redundancy: 6.68 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.33 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo-LUSH

Resolution: 1.4→41.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20283 5618 10.1 %RANDOM
Rwork0.17491 ---
obs0.17768 50190 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 49 416 2599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222245
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9893026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3324.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10215418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8851512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021711
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.31156
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.51565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.5538
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.568
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.51365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07722221
X-RAY DIFFRACTIONr_scbond_it1.8832880
X-RAY DIFFRACTIONr_scangle_it3.1513805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 419 -
Rwork0.193 3627 -
obs--99.88 %

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