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

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Basic information

Entry
Database: PDB / ID: 3cab
TitleCrystal structure of a pheromone binding protein from Apis mellifera soaked at pH 7.0
ComponentsPheromone-binding protein ASP1
KeywordsPHEROMONE-BINDING PROTEIN / honeybee / Apis mellifera / pheromone binding protein / signal transduction / queen mandibular pheromone
Function / homology
Function and homology information


dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / 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
Odorant binding protein ASP1 / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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
DepositionFeb 19, 2008Deposition 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)13,4714
Polymers13,1951
Non-polymers2763
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.478, 86.185, 49.557
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-124-

HOH

21A-134-

HOH

31A-147-

HOH

41A-167-

HOH

51A-210-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, crystal was soaked in same conditions at pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2007 / Details: cylindrical gazing incidence mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→56.8 Å / Num. all: 12126 / Num. obs: 12126 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 29.57 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1733 / Rsym value: 0.413 / % 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 3BJH

3bjh


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.921 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21714 976 8.1 %RANDOM
Rwork0.17511 ---
all0.17848 11121 --
obs0.17848 11121 99.88 %-
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: 37.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---1.77 Å20 Å2
3---1.59 Å2
Refine analyzeLuzzati coordinate error free: 0.134 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 18 112 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022956
X-RAY DIFFRACTIONr_bond_other_d0.0020.02628
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9811301
X-RAY DIFFRACTIONr_angle_other_deg0.9483.0081549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11427.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15115162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.026152
X-RAY DIFFRACTIONr_chiral_restr0.0860.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
X-RAY DIFFRACTIONr_nbd_refined0.2130.2249
X-RAY DIFFRACTIONr_nbd_other0.190.2608
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2483
X-RAY DIFFRACTIONr_nbtor_other0.0910.2448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.217
X-RAY DIFFRACTIONr_mcbond_it0.8121.5770
X-RAY DIFFRACTIONr_mcbond_other0.1931.5235
X-RAY DIFFRACTIONr_mcangle_it1.0112965
X-RAY DIFFRACTIONr_scbond_it1.5593411
X-RAY DIFFRACTIONr_scangle_it2.1644.5334
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 61 -
Rwork0.215 802 -
obs--99.88 %
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)
11.7927-0.50171.17482.6682-1.61845.0657-0.03120.09650.40890.0874-0.2843-0.281-0.38780.52440.3155-0.2055-0.0434-0.0131-0.18240.0135-0.100511.35911.7451-4.6732
213.98792.5724-3.76354.70530.68614.3957-0.24580.4414-0.2822-0.11010.281-0.4232-0.00280.3033-0.0352-0.0036-0.1159-0.03060.0747-0.0995-0.095319.776818.15129.4095
34.24991.43893.614713.00355.342410.667-0.3117-0.03030.4949-0.35830.08170.0549-0.99240.41670.23-0.157-0.02990.0069-0.1335-0.0207-0.11817.27715.06244.8703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 693 - 69
2X-RAY DIFFRACTION2AA70 - 8870 - 88
3X-RAY DIFFRACTION3AA89 - 11989 - 119

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