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

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Basic information

Entry
Database: PDB / ID: 3cyz
TitleDimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0
ComponentsPheromone-binding protein ASP1
KeywordsPheromone Binding Protein / honeybee / Apis mellifera / signal transduction / queen mandibular pheromone
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
(2Z)-9-oxodec-2-enoic acid / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Advisory / 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 1.3Nov 13, 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)27,29312
Polymers26,3902
Non-polymers90310
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-58.2 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.285, 75.555, 84.113
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, 309 molecules

#2: Chemical ChemComp-9OD / (2Z)-9-oxodec-2-enoic acid / 9-keto-2(E)-decenoic acid


Mass: 184.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M magnesium chloride, 0.1M Tris, 15% PEG8000, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2007 / Details: cylindrical gazing incidence mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→84.25 Å / Num. all: 21263 / Num. obs: 21263 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.97 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2614 / Rsym value: 0.457 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BJH

3bjh


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.495 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19964 1057 5 %RANDOM
Rwork0.16181 ---
all0.16372 20184 --
obs0.16372 20184 96.03 %-
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: 16.682 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---1.69 Å20 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error free: 0.124 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 56 299 2139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221953
X-RAY DIFFRACTIONr_bond_other_d0.0040.021299
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9952663
X-RAY DIFFRACTIONr_angle_other_deg1.0283.0073219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8365247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80427.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1415338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.937154
X-RAY DIFFRACTIONr_chiral_restr0.080.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02328
X-RAY DIFFRACTIONr_nbd_refined0.2390.2505
X-RAY DIFFRACTIONr_nbd_other0.2040.21379
X-RAY DIFFRACTIONr_nbtor_refined0.180.2958
X-RAY DIFFRACTIONr_nbtor_other0.0910.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.231
X-RAY DIFFRACTIONr_mcbond_it0.7991.51536
X-RAY DIFFRACTIONr_mcbond_other0.2091.5470
X-RAY DIFFRACTIONr_mcangle_it0.96521954
X-RAY DIFFRACTIONr_scbond_it1.8353855
X-RAY DIFFRACTIONr_scangle_it2.6544.5700
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 69 -
Rwork0.196 1107 -
obs-1107 73.96 %
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)
14.56360.5582-3.16554.11770.82623.25120.1535-0.022-0.0211-0.2176-0.0399-0.1719-0.18580.2535-0.1136-0.02880.000900.0011-0.0094-0.018623.3778-8.05542.5707
24.5691-0.3914-0.87814.48041.01537.019-0.1180.0201-0.0023-0.24320.176-0.30260.21460.3517-0.0580.0409-0.02020.04350.00450.00770.047134.4999-9.8961-24.8016
30.0218-0.0859-0.05990.6134-0.30071.2106-0.0351-0.0583-0.02790.04570.0369-0.0535-0.0791-0.011-0.0017-0.03950.0055-0.0027-0.0297-0.0066-0.022717.7278-1.2771-5.0697
40.3676-0.23620.10240.7996-0.21150.56260.0002-0.0010.0299-0.08220.0106-0.0219-0.0370.0255-0.0108-0.0293-0.01080.0067-0.03250.0028-0.032324.4455-17.199-22.2522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB5 - 115 - 11
2X-RAY DIFFRACTION1AA114 - 119114 - 119
3X-RAY DIFFRACTION2AA4 - 114 - 11
4X-RAY DIFFRACTION2BB114 - 119114 - 119
5X-RAY DIFFRACTION3AA12 - 11312 - 113
6X-RAY DIFFRACTION4BB12 - 11312 - 113

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