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- PDB-3bfa: Crystal structure of a pheromone binding protein from Apis mellif... -

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Basic information

Entry
Database: PDB / ID: 3bfa
TitleCrystal structure of a pheromone binding protein from Apis mellifera in complex with the Queen mandibular pheromone
ComponentsPheromone-binding protein ASP1
KeywordsPHEROMONE BINDING PROTEIN / Honeybee / Apis mellifera / Signal transduction / Queen mandibular pheromone / PHEROMONE-BINDING PROTEIN
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular space / 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
(2Z)-9-oxodec-2-enoic acid / Odorant binding protein ASP1 / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis of the honey bee PBP pheromone and pH-induced conformational change
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_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
Revision 1.3Oct 16, 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: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4713
Polymers13,1951
Non-polymers2762
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.461, 85.019, 48.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

21A-127-

HOH

31A-195-

HOH

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Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13194.789 Da / Num. of mol.: 1 / Fragment: UNP residues 26-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Plasmid: pHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9U9J6, UniProt: Q8WRW5*PLUS
#2: Chemical ChemComp-9OD / (2Z)-9-oxodec-2-enoic acid / 9-keto-2(E)-decenoic acid


Mass: 184.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.8M ammonium sulphate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 9, 2007 / Details: Tiroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.25→57.3 Å / Num. all: 7888 / Num. obs: 7888 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 43.67 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 16.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1119 / Rsym value: 0.518 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5R

1r5r
PDB Unreleased entry


Resolution: 2.25→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.065 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23581 769 9.8 %RANDOM
Rwork0.18059 ---
all0.18598 7107 --
obs0.18598 7107 99.95 %-
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: 55.524 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.65 Å20 Å2
3----0.4 Å2
Refine analyzeLuzzati coordinate error free: 0.207 Å
Refinement stepCycle: LAST / Resolution: 2.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 19 75 1001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022947
X-RAY DIFFRACTIONr_bond_other_d0.0010.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9851286
X-RAY DIFFRACTIONr_angle_other_deg0.9153.0081527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4065116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64527.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6915159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.36152
X-RAY DIFFRACTIONr_chiral_restr0.070.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02160
X-RAY DIFFRACTIONr_nbd_refined0.2250.2252
X-RAY DIFFRACTIONr_nbd_other0.1880.2608
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2482
X-RAY DIFFRACTIONr_nbtor_other0.0890.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.29
X-RAY DIFFRACTIONr_mcbond_it0.6331.5760
X-RAY DIFFRACTIONr_mcbond_other0.1341.5233
X-RAY DIFFRACTIONr_mcangle_it0.7872953
X-RAY DIFFRACTIONr_scbond_it1.3853408
X-RAY DIFFRACTIONr_scangle_it1.9054.5333
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 52 -
Rwork0.226 514 -
obs-514 99.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2208-0.23962.20083.4359-1.05557.4023-0.03680.06290.6438-0.1663-0.1695-0.4876-0.35820.74310.2063-0.2096-0.04460.0425-0.20550.0211-0.097511.005412.2469-5.7937
26.3824-0.08243.29255.54791.82168.9736-0.215-0.4330.97540.24950.0058-0.514-1.09640.95220.20920.0041-0.202-0.02630.0029-0.0807-0.044712.543115.36717.1485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 623 - 62
2X-RAY DIFFRACTION2AA63 - 11963 - 119

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