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- PDB-3cz1: Dimeric crystal structure of a pheromone binding protein from Api... -

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Basic information

Entry
Database: PDB / ID: 3cz1
TitleDimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with the n-butyl benzene sulfonamide at pH 7.0
ComponentsPheromone-binding protein ASP1
KeywordsPheromone Binding Protein / Honey bee / signal transduction / queen mandibular pheromone
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: 1.5 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
CitationJournal: 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.
History
DepositionApr 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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)27,43612
Polymers26,3902
Non-polymers1,04710
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-47.7 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.413, 75.652, 84.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pheromone-binding protein ASP1


Mass: 13194.789 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-NBB / N-BUTYL-BENZENESULFONAMIDE


Mass: 213.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15NO2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.2M magnesium chloride, 0.1M Tris, 15% PEG8000, pH6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006 / Details: Tiroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.5→56.25 Å / Num. all: 36737 / Num. obs: 36737 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.21 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5313 / Rsym value: 0.301 / % possible all: 100

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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 3CYZ

3cyz


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.443 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19844 1144 3.1 %RANDOM
Rwork0.1518 ---
all0.15331 35532 --
obs0.15331 35532 99.13 %-
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: 12.421 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.76 Å20 Å2
3----0.31 Å2
Refine analyzeLuzzati coordinate error free: 0.075 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 64 280 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221977
X-RAY DIFFRACTIONr_bond_other_d0.0020.021329
X-RAY DIFFRACTIONr_angle_refined_deg1.6012.0032695
X-RAY DIFFRACTIONr_angle_other_deg1.5553.0073287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.22426.92391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72215352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.88155
X-RAY DIFFRACTIONr_chiral_restr0.210.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_nbd_refined0.2580.2454
X-RAY DIFFRACTIONr_nbd_other0.20.21336
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2990
X-RAY DIFFRACTIONr_nbtor_other0.0910.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4341.51537
X-RAY DIFFRACTIONr_mcbond_other0.4831.5468
X-RAY DIFFRACTIONr_mcangle_it1.81921970
X-RAY DIFFRACTIONr_scbond_it2.6283886
X-RAY DIFFRACTIONr_scangle_it3.4794.5719
X-RAY DIFFRACTIONr_rigid_bond_restr1.29934003
X-RAY DIFFRACTIONr_sphericity_free6.083284
X-RAY DIFFRACTIONr_sphericity_bonded2.40733265
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 80 -
Rwork0.165 2613 -
obs-2613 99.89 %

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