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- PDB-3d76: Crystal structure of a pheromone binding protein mutant D35N, fro... -

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Basic information

Entry
Database: PDB / ID: 3d76
TitleCrystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, soaked 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 / FOURIER SYNTHESIS / Resolution: 1.9 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 1.4Nov 20, 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)13,8029
Polymers13,1941
Non-polymers6098
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.991, 84.196, 47.558
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-132-

HOH

21A-133-

HOH

31A-134-

HOH

41A-187-

HOH

51A-199-

HOH

61A-231-

HOH

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Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13193.804 Da / Num. of mol.: 1 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NBB / N-BUTYL-BENZENESULFONAMIDE


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


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


Mass: 18.015 Da / Num. of mol.: 130 / 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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, crystal was soaked in the same condition at pH7.0, 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 22, 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: 1.9→25.13 Å / Num. all: 12833 / Num. obs: 12833 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 22.88 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1837 / Rsym value: 0.322 / % 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 3D75

3d75


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.773 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24146 947 7.5 %RANDOM
Rwork0.19044 ---
all0.19423 11728 --
obs0.19423 11728 98.85 %-
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: 26.522 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.11 Å2
Refine analyzeLuzzati coordinate error free: 0.144 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 39 130 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022956
X-RAY DIFFRACTIONr_bond_other_d0.0020.02638
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9921292
X-RAY DIFFRACTIONr_angle_other_deg1.2763.0081563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67527.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01915156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.491152
X-RAY DIFFRACTIONr_chiral_restr0.290.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.2310.2287
X-RAY DIFFRACTIONr_nbd_other0.2090.2716
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2483
X-RAY DIFFRACTIONr_nbtor_other0.0950.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.218
X-RAY DIFFRACTIONr_mcbond_it0.6261.5584
X-RAY DIFFRACTIONr_mcbond_other0.1621.5231
X-RAY DIFFRACTIONr_mcangle_it1.052948
X-RAY DIFFRACTIONr_scbond_it1.6383385
X-RAY DIFFRACTIONr_scangle_it2.5724.5343
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.583 65 -
Rwork0.499 778 -
obs-778 91.93 %

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