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- PDB-3d74: Crystal structure of a pheromone binding protein mutant D35A, fro... -

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Basic information

Entry
Database: PDB / ID: 3d74
TitleCrystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, soaked at pH 5.5
ComponentsPheromone-binding protein ASP1
KeywordsPheromone Binding Protein / Honey bee / Apis mellifera / signal transduction / queen mandibular protein / pH
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
N-BUTYL-BENZENESULFONAMIDE / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 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)26,9415
Polymers26,3022
Non-polymers6403
Water2,198122
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)13,3642
Polymers13,1511
Non-polymers2131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5773
Polymers13,1511
Non-polymers4272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.133, 60.769, 56.270
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-124-

HOH

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Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13150.778 Da / Num. of mol.: 2 / Fragment: UNP residues 26-144 / Mutation: D35A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, crystal was soaked in the same condition at pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 21, 2008 / Details: polar mirror
RadiationMonochromator: Osmic vacuum / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.1→30.39 Å / Num. all: 12708 / Num. obs: 12708 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.26 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1804 / Rsym value: 0.29 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3D73

3d73


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.61 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22921 949 7.5 %RANDOM
Rwork0.17472 ---
all0.17886 11717 --
obs0.17886 11717 99.63 %-
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: 28.728 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---2.3 Å20 Å2
3----0.31 Å2
Refine analyzeLuzzati coordinate error free: 0.205 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 42 122 2009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221930
X-RAY DIFFRACTIONr_bond_other_d0.0080.021253
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9932637
X-RAY DIFFRACTIONr_angle_other_deg1.0043.0083087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1545242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5527.07989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85115314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.016154
X-RAY DIFFRACTIONr_chiral_restr0.10.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined0.2330.2465
X-RAY DIFFRACTIONr_nbd_other0.20.21250
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2973
X-RAY DIFFRACTIONr_nbtor_other0.0890.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.216
X-RAY DIFFRACTIONr_mcbond_it0.8811.51548
X-RAY DIFFRACTIONr_mcbond_other0.1581.5475
X-RAY DIFFRACTIONr_mcangle_it0.86721953
X-RAY DIFFRACTIONr_scbond_it2.0483831
X-RAY DIFFRACTIONr_scangle_it2.5094.5681
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 65 -
Rwork0.229 823 -
obs-823 100 %

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