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- PDB-3fe8: Crystal structure of a pheromone binding protein from Apis mellif... -

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Basic information

Entry
Database: PDB / ID: 3fe8
TitleCrystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 4.0
ComponentsPheromone-binding protein ASP1
KeywordsPheromone binding protein / honey bee / Apis mellifera / signal transduction / queen mandibular protein / pH
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular space
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
(20S)-20-methyldotetracontane / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 1.3Nov 6, 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
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.374, 84.671, 46.263
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-181-

HOH

41A-239-

HOH

51A-271-

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.: 157 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.7M ammonium sulfate, 0.1M sodium citrate, pH4.0, 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: 1.9→46.27 Å / Num. all: 13139 / Num. obs: 13139 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1893 / Rsym value: 0.464 / % 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 3CYZ

3cyz


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.114 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20243 987 7.5 %RANDOM
Rwork0.16283 ---
all0.16574 12133 --
obs0.16574 12133 99.99 %-
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: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error free: 0.122 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 50 157 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221015
X-RAY DIFFRACTIONr_bond_other_d0.0030.02718
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.0131377
X-RAY DIFFRACTIONr_angle_other_deg2.7583.0071780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.1495128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86727.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5815164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.414152
X-RAY DIFFRACTIONr_chiral_restr0.1190.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211094
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02162
X-RAY DIFFRACTIONr_mcbond_it0.5371.5613
X-RAY DIFFRACTIONr_mcbond_other0.1591.5240
X-RAY DIFFRACTIONr_mcangle_it1.02521002
X-RAY DIFFRACTIONr_scbond_it1.8093402
X-RAY DIFFRACTIONr_scangle_it2.784.5370
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 82 -
Rwork0.193 858 -
obs-858 100 %
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)
11.0148-0.2726-0.10140.9503-0.20731.3869-0.0737-0.0201-0.12620.03830.0081-0.06590.12290.070.06560.04190.0090.00820.0422-0.00650.058-29.1403-12.5035-15.4871
22.445-0.850.81263.78291.36111.5166-0.07560.0768-0.1303-0.0998-0.0720.1719-0.03830.10980.14770.14510.0168-0.02710.09860.05740.0931-24.4601-21.6163-2.584
33.4927-1.6852-0.9523.2581-1.19843.0526-0.05-0.1592-0.07630.2622-0.1502-0.2022-0.04660.07110.20030.0414-0.0087-0.0460.0460.02420.0606-25.4036-8.3766-6.5542
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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