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- PDB-3bjh: Soft-SAD crystal structure of a pheromone binding protein from th... -

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Basic information

Entry
Database: PDB / ID: 3bjh
TitleSoft-SAD crystal structure of a pheromone binding protein from the honeybee Apis mellifera L.
ComponentsPheromone-binding protein ASP1
KeywordsPHEROMONE BINDING PROTEIN / Honeybee / Apis mellifera / signal transduction
Function / homology
Function and homology information


odorant binding / 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
N-BUTYL-BENZENESULFONAMIDE / Odorant binding protein ASP1 / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLartigue, A. / Gruez, A. / Briand, L. / Blon, F. / Bezirard, V. / Walsh, M. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L.
Authors: Lartigue, A. / Gruez, A. / Briand, L. / Blon, F. / Walsh, M. / 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
DepositionDec 4, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 18, 2007ID: 1R5R
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)13,5003
Polymers13,1951
Non-polymers3052
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.386, 86.289, 50.698
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-221-

HOH

21A-229-

HOH

31A-260-

HOH

41A-261-

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-NBB / N-BUTYL-BENZENESULFONAMIDE


Mass: 213.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO2S
#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.: 158 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5M ammonium sulfate, 0.15M sodium citrate, pH5.5, VAPOR DIFFUSION, HANGING 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: Jul 23, 2002 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→37.8 Å / Num. obs: 22274 / % possible obs: 99.6 % / Observed criterion σ(F): 5.4 / Redundancy: 5.2 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.85 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20645 2234 10.1 %RANDOM
Rwork0.17147 ---
obs0.17495 19846 99.5 %-
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: 32.369 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2---1 Å20 Å2
3----1.51 Å2
Refine analyzeLuzzati coordinate error free: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 20 158 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022954
X-RAY DIFFRACTIONr_bond_other_d0.0020.02622
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9921298
X-RAY DIFFRACTIONr_angle_other_deg1.7983.0081534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68827.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95415162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.103152
X-RAY DIFFRACTIONr_chiral_restr0.0760.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.2240.2217
X-RAY DIFFRACTIONr_nbd_other0.1850.2603
X-RAY DIFFRACTIONr_nbtor_refined0.180.2477
X-RAY DIFFRACTIONr_nbtor_other0.0910.2469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.222
X-RAY DIFFRACTIONr_mcbond_it0.7981.5760
X-RAY DIFFRACTIONr_mcbond_other0.1991.5233
X-RAY DIFFRACTIONr_mcangle_it1.0132957
X-RAY DIFFRACTIONr_scbond_it1.5133418
X-RAY DIFFRACTIONr_scangle_it1.9684.5341
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 166 -
Rwork0.191 1442 -
obs-1442 99.57 %
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)
11.5644-0.71310.78832.8798-2.12844.9897-0.02790.03820.24140.1621-0.2743-0.3601-0.4160.62790.3022-0.3563-0.0691-0.0238-0.18210.0241-0.173811.40811.725-4.917
214.49870.1734-5.07351.49050.77522.8145-0.42480.4353-0.5238-0.24420.2436-0.25490.4237-0.02920.1812-0.1521-0.22360.00810.1391-0.1039-0.084919.5618.7039.203
35.48721.64131.53498.72891.84796.7579-0.1126-0.13970.3552-0.004-0.0213-0.1606-0.88390.33050.1339-0.2494-0.0569-0.0074-0.1862-0.0156-0.21387.06515.6694.537
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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