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- PDB-3b6x: Complex of S52A Substituted Drosophila LUSH protein with Butanol -

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Basic information

Entry
Database: PDB / ID: 3b6x
TitleComplex of S52A Substituted Drosophila LUSH protein with Butanol
ComponentsGeneral odorant-binding protein lush
KeywordsTRANSPORT PROTEIN / Odorant Binding / Alcohol Binding / 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
1-BUTANOL / ACETATE ION / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsThode, A.B. / Jones, D.N.M.
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 29, 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 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 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
A: General odorant-binding protein lush
B: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1199
Polymers28,6752
Non-polymers4437
Water4,576254
1
A: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4713
Polymers14,3381
Non-polymers1332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: General odorant-binding protein lush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6486
Polymers14,3381
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.872, 46.872, 111.327
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 General odorant-binding protein lush


Mass: 14337.656 Da / Num. of mol.: 2 / Fragment: Chain A / Mutation: Serine 52 to Alanine
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Fragment: Chain B / Mutation: Serine 52 to Alanine / 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.: 254 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 400, 100mM Sodium Acetate, 3:1 protein/well ratio, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature Room tempK, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2003
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 15934 / Num. obs: 15795 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.02 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.329 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1088 / Rsym value: 0.214 / Χ2: 1.436 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OOH

1ooh


Resolution: 2→29.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.885 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.238 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1592 10.1 %RANDOM
Rwork0.163 ---
all0.187 ---
obs0.169 15795 99.14 %-
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: 21.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.193 Å
Refinement stepCycle: LAST / Resolution: 2→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 29 254 2269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222152
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9752895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4515266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40724.28698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68315402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8171514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021646
X-RAY DIFFRACTIONr_nbd_refined0.2010.21102
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.222
X-RAY DIFFRACTIONr_mcbond_it1.49521384
X-RAY DIFFRACTIONr_mcangle_it2.03432139
X-RAY DIFFRACTIONr_scbond_it2.6673870
X-RAY DIFFRACTIONr_scangle_it3.7674756
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 116 -
Rwork0.162 1062 -
all-1178 -
obs--98.25 %

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