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- PDB-3cz2: Dimeric crystal structure of a pheromone binding protein from Api... -

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Basic information

Entry
Database: PDB / ID: 3cz2
TitleDimeric crystal structure of a pheromone binding protein from Apis mellifera at pH 7.0
ComponentsPheromone-binding protein ASP1
KeywordsPheromone Binding Protein / Honey bee / Apis mellifera / signal transduction / queen mandibular protein
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
Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)26,6389
Polymers26,3902
Non-polymers2487
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-82.8 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.862, 75.513, 84.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B
21A B
31A B
41A B
51A B
61A B
71A B
81A B
91A B
101A B
111A B
121A B
131A B
141A B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALHISHISAA13 - 2413 - 24
21VALVALHISHISBB13 - 2413 - 24
32ALAALALYSLYSAA29 - 3629 - 36
42ALAALALYSLYSBB29 - 3629 - 36
53GLUGLUPHEPHEAA42 - 5642 - 56
63GLUGLUPHEPHEBB42 - 5642 - 56
74ASPASPGLYGLYAA66 - 7266 - 72
84ASPASPGLYGLYBB66 - 7266 - 72
95GLNGLNCYSCYSAA79 - 8979 - 89
105GLNGLNCYSCYSBB79 - 8979 - 89
116CYSCYSGLYGLYAA89 - 9489 - 94
126CYSCYSGLYGLYBB89 - 9489 - 94
137ASNASNALAALAAA97 - 11297 - 112
147ASNASNALAALABB97 - 11297 - 112

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Components

#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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Magnesium chloride, 0.1M Tris, 17% 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: ID23-1 / Wavelength: 0.886 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2006 / Details: Tiroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 8426 / Num. obs: 8426 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 30.15 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1214 / Rsym value: 0.313 / % 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 3CZY

3czy


Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.842 / SU B: 22.179 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.617 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27838 826 9.8 %RANDOM
Rwork0.22017 ---
all0.22578 7568 --
obs0.22578 7568 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.893 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2---1.54 Å20 Å2
3----0.31 Å2
Refine analyzeLuzzati coordinate error free: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 7 23 1843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221849
X-RAY DIFFRACTIONr_bond_other_d0.0060.021194
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.972522
X-RAY DIFFRACTIONr_angle_other_deg0.8663.0082941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27227.07989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.888154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
X-RAY DIFFRACTIONr_nbd_refined0.2120.2415
X-RAY DIFFRACTIONr_nbd_other0.1840.21161
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2935
X-RAY DIFFRACTIONr_nbtor_other0.0870.2883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0380.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.51501
X-RAY DIFFRACTIONr_mcbond_other0.1011.5465
X-RAY DIFFRACTIONr_mcangle_it0.65921899
X-RAY DIFFRACTIONr_scbond_it1.2753773
X-RAY DIFFRACTIONr_scangle_it1.8024.5623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 970 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.60.5
medium thermal0.482
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 55 -
Rwork0.284 561 -
obs-561 100 %

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