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- PDB-1ooh: Complex of Drosophila odorant binding protein LUSH with butanol -

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Basic information

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


diphenyl phthalate binding / dibutyl phthalate binding / courtship behavior / response to pheromone / olfactory behavior / 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
1-BUTANOL / ACETATE ION / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,2668
Polymers28,8812
Non-polymers3846
Water5,927329
1
A: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6334
Polymers14,4411
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6334
Polymers14,4411
Non-polymers1923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.938, 46.938, 111.328
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: 14440.732 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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, n-butanol, 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: 1.25→30 Å / Num. all: 66271 / Num. obs: 64084 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 21.8
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5918 / % possible all: 89.4
Reflection
*PLUS
Num. measured all: 196015
Reflection shell
*PLUS
% possible obs: 89.4 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OOF

1oof


Resolution: 1.25→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.941 / SU ML: 0.044 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18501 6344 10.1 %RANDOM
Rwork0.16044 ---
all0.16294 59607 --
obs0.16294 56323 94.49 %-
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: 11.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 26 329 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222151
X-RAY DIFFRACTIONr_bond_other_d0.0010.021944
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.9752879
X-RAY DIFFRACTIONr_angle_other_deg0.74334593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5433250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.59315458
X-RAY DIFFRACTIONr_chiral_restr0.0790.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
X-RAY DIFFRACTIONr_nbd_refined0.2410.3521
X-RAY DIFFRACTIONr_nbd_other0.2080.31869
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.5197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.548
X-RAY DIFFRACTIONr_mcbond_it0.771.51295
X-RAY DIFFRACTIONr_mcangle_it1.34422101
X-RAY DIFFRACTIONr_scbond_it1.923856
X-RAY DIFFRACTIONr_scangle_it3.0974.5778
X-RAY DIFFRACTIONr_rigid_bond_restr0.94722151
X-RAY DIFFRACTIONr_sphericity_free1.9732329
X-RAY DIFFRACTIONr_sphericity_bonded1.55422107
LS refinement shellResolution: 1.25→1.318 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.202 828
Rwork0.171 7311
obs-8073
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.315

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