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- PDB-3b7a: Complex of S52A Substituted Droposphila LUSH protein with Ethanol -

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Basic information

Entry
Database: PDB / ID: 3b7a
TitleComplex of S52A Substituted Droposphila LUSH protein with Ethanol
ComponentsGeneral odorant-binding protein lush
KeywordsTRANSPORT PROTEIN / Odorant Binding Protein / Alochol Binding Protein / Behavior / Olfaction / Pheromone response / Pheromone-binding / Secreted / Sensory transduction / Transport
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
ACETATE ION / ETHANOL / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJones, D.N.M. / Thode, A.B.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The role of multiple hydrogen-bonding groups in specific alcohol binding sites in proteins: insights from structural studies of LUSH.
Authors: Thode, A.B. / Kruse, S.W. / Nix, J.C. / Jones, D.N.
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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: General odorant-binding protein lush
B: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7408
Polymers28,3992
Non-polymers3416
Water2,594144
1
A: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2462
Polymers14,2001
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General odorant-binding protein lush


Theoretical massNumber of molelcules
Total (without water)14,2001
Polymers14,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.873, 46.873, 111.206
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein General odorant-binding protein lush / lush / Obp76a / Obp76c


Mass: 14199.508 Da / Num. of mol.: 2 / Mutation: S52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lush, Obp76a, Obp76c / Production host: Escherichia coli (E. coli) / References: UniProt: O02372
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Mutation: S52A / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 295 K / pH: 4.6
Details: 25% PEG 4000, 100mM Sodium Acetate, 3:1 protein/well solution, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.12 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→35.76 Å / Num. obs: 25896 / % possible obs: 98.9 % / Redundancy: 3.35 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Phasing

Phasing MRRfactor: 0.34 / Cor.coef. Fo:Fc: 0.705
Highest resolutionLowest resolution
Rotation3.5 Å35.84 Å
Translation3.5 Å35.84 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OOH

1ooh


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.762 / SU ML: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.236 1891 10.2 %
Rwork0.198 --
obs0.202 18492 98.5 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 29.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 27 144 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.982856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55624.22797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99115401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5741515
X-RAY DIFFRACTIONr_chiral_restr0.0760.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21000
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.61821350
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37232110
X-RAY DIFFRACTIONr_scbond_it2.673854
X-RAY DIFFRACTIONr_scangle_it3.7914745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.297 166 -
Rwork0.231 1228 -
obs--99.43 %

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