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- PDB-3fe9: Crystal structure of a pheromone binding protein from Apis mellif... -

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Basic information

Entry
Database: PDB / ID: 3fe9
TitleCrystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 7.0
ComponentsPheromone-binding protein ASP1
KeywordsPheromone binding protein / honey bee / Apis mellifera / signal transduction / queen mandibular protein
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: 1.75 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 28, 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)13,8353
Polymers13,1951
Non-polymers6412
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.298, 83.909, 46.804
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-122-

HOH

21A-124-

HOH

31A-300-

HOH

41A-408-

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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 159 / 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: 60.31 %
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: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→41.96 Å / Num. all: 16926 / Num. obs: 16926 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 21.99 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 21.2
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2441 / Rsym value: 0.484 / % 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 2H8V

2h8v


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.743 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18689 992 5.9 %RANDOM
Rwork0.16084 ---
all0.16238 15916 --
obs0.16238 15916 99.89 %-
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: 11.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3----0.15 Å2
Refine analyzeLuzzati coordinate error free: 0.089 Å
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 44 159 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022998
X-RAY DIFFRACTIONr_bond_other_d0.0010.02702
X-RAY DIFFRACTIONr_angle_refined_deg1.2772.0061351
X-RAY DIFFRACTIONr_angle_other_deg1.2083.0071743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40427.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75215169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.02152
X-RAY DIFFRACTIONr_chiral_restr0.0830.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02160
X-RAY DIFFRACTIONr_mcbond_it0.6321.5599
X-RAY DIFFRACTIONr_mcbond_other0.1941.5235
X-RAY DIFFRACTIONr_mcangle_it1.1412981
X-RAY DIFFRACTIONr_scbond_it1.8353399
X-RAY DIFFRACTIONr_scangle_it2.8394.5367
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 85 -
Rwork0.189 1152 -
obs-1152 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)
11.55660.02620.87871.8156-0.4432.52040.03210.00720.193-0.0016-0.1313-0.2048-0.03940.20030.09920.0437-0.01510.01930.03310.01260.079511.806811.7647-4.1581
21.32651.0099-0.06971.38640.78663.5064-0.03830.0671-0.2083-0.0272-0.1159-0.4069-0.26840.29030.15430.2159-0.1073-0.09170.3287-0.09010.276620.998217.00619.1103
33.78550.75061.59984.9999-1.71263.8583-0.2533-0.54190.42210.2693-0.0874-0.2344-0.28930.02290.34070.0869-0.0126-0.03910.092-0.07390.09728.139215.71924.966
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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