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- PDB-3fe6: Crystal structure of a pheromone binding protein from Apis mellif... -

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Basic information

Entry
Database: PDB / ID: 3fe6
TitleCrystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand at pH 5.5
ComponentsPheromone-binding protein ASP1
KeywordsPheromone binding protein / honey bee / Apis mellifera / signal transduction / queen mandibular pheromone / pH
Function / homology
Function and homology information


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
(20S)-20-methyldotetracontane / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
Citation
Journal: To be Published
Title: Queen bee pheromone binding protein pH induced domain-swapping favors pheromone release
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
#1: Journal: 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 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: 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 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: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9274
Polymers13,1951
Non-polymers7333
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.879, 84.210, 46.831
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-126-

HOH

31A-214-

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
#2: Chemical ChemComp-CMJ / (20S)-20-methyldotetracontane


Mass: 605.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H88
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.7M ammonium sulfate, 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2007 / Details: Tiroidal mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→42.11 Å / Num. all: 15535 / Num. obs: 15535 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 23.17 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 22.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2231 / Rsym value: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.4.0077phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5R

1r5r
PDB Unreleased entry


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.16 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19289 1111 7.2 %RANDOM
Rwork0.15871 ---
all0.16112 14409 --
obs0.16112 14409 99.71 %-
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: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2--0.41 Å20 Å2
3----0.36 Å2
Refine analyzeLuzzati coordinate error free: 0.099 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 50 150 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022989
X-RAY DIFFRACTIONr_bond_other_d0.0090.02693
X-RAY DIFFRACTIONr_angle_refined_deg1.3652.0071337
X-RAY DIFFRACTIONr_angle_other_deg1.5693.0071715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56927.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.315160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.052152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211064
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02160
X-RAY DIFFRACTIONr_mcbond_it0.6461.5595
X-RAY DIFFRACTIONr_mcbond_other0.2241.5235
X-RAY DIFFRACTIONr_mcangle_it1.1442969
X-RAY DIFFRACTIONr_scbond_it1.9993394
X-RAY DIFFRACTIONr_scangle_it3.0694.5365
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 62 -
Rwork0.208 1077 -
obs--100 %
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)
11.63610.07710.61211.8929-0.34792.3980.0365-0.01070.189-0.0304-0.1348-0.2172-0.04940.19920.09830.0645-0.01550.01950.05370.01330.085411.633111.7462-4.0179
20.30530.44640.71361.5993-0.23263.3877-0.07910.0472-0.2190.0998-0.1085-0.3578-0.18160.26750.18760.1903-0.1056-0.09640.3456-0.11560.276320.922717.07439.1356
33.96310.65411.37414.5162-1.51144.0685-0.212-0.48410.42140.3372-0.053-0.1758-0.24640.03780.2650.0883-0.0135-0.04320.0974-0.07220.08638.311315.74475.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 69
2X-RAY DIFFRACTION2A70 - 88
3X-RAY DIFFRACTION3A89 - 119

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