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- PDB-3d78: Dimeric crystal structure of a pheromone binding protein mutant D... -

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Basic information

Entry
Database: PDB / ID: 3d78
TitleDimeric crystal structure of a pheromone binding protein mutant D35N, from apis mellifera, at pH 7.0
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
N-BUTYL-BENZENESULFONAMIDE / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Mol.Biol. / Year: 2009
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. / Campanacci, V. / Tegoni, M. / Cambillau, C.
#1: Journal: To be Published
Title: The pH Driven Domain-swapping Dimerization of Queen Bee ASP1 Favours Pheromone Release
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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
B: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,40011
Polymers26,3882
Non-polymers1,0129
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7177
Polymers13,1941
Non-polymers5246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6824
Polymers13,1941
Non-polymers4893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.054, 60.948, 57.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-190-

HOH

21B-218-

HOH

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Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13193.804 Da / Num. of mol.: 2 / Fragment: UNP residues 26-144 / Mutation: D35N
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-NBB / N-BUTYL-BENZENESULFONAMIDE


Mass: 213.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15NO2S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.1M ammonium sulfate, 0.2M di ammonium phosphate, 20mM di sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2008 / Details: Tiroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 32103 / Num. obs: 32103 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4588 / Rsym value: 0.321 / % possible all: 99.6

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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 3D73

3d73


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.57 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20597 1200 4.1 %RANDOM
Rwork0.15897 ---
all0.16088 28039 --
obs0.16088 28039 99.54 %-
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: 21.421 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20 Å2
2---2.08 Å20 Å2
3---0.91 Å2
Refine analyzeLuzzati coordinate error free: 0.094 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 66 242 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222021
X-RAY DIFFRACTIONr_bond_other_d0.0020.021333
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9952766
X-RAY DIFFRACTIONr_angle_other_deg0.9853.0073293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3045263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60527.09793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0115335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.447154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
X-RAY DIFFRACTIONr_nbd_refined0.2390.2466
X-RAY DIFFRACTIONr_nbd_other0.2040.21370
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21026
X-RAY DIFFRACTIONr_nbtor_other0.0860.2938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.230
X-RAY DIFFRACTIONr_mcbond_it1.2611.51611
X-RAY DIFFRACTIONr_mcbond_other0.4341.5485
X-RAY DIFFRACTIONr_mcangle_it1.56222022
X-RAY DIFFRACTIONr_scbond_it2.5463897
X-RAY DIFFRACTIONr_scangle_it3.1874.5730
X-RAY DIFFRACTIONr_rigid_bond_restr1.29834128
X-RAY DIFFRACTIONr_sphericity_free6.1283246
X-RAY DIFFRACTIONr_sphericity_bonded2.27233304
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 83 -
Rwork0.151 2026 -
obs-2026 99.86 %

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