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- PDB-2h8v: Structure of empty Pheromone Binding Protein ASP1 from the Honeyb... -

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Basic information

Entry
Database: PDB / ID: 2h8v
TitleStructure of empty Pheromone Binding Protein ASP1 from the Honeybee Apis mellifera L
ComponentsPheromone-binding protein ASP1
KeywordsTRANSPORT PROTEIN / PHEROMONE / HONEY BEE
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular space / extracellular region
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
Odorant binding protein ASP1 / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPesenti, M.E. / Spinelli, S. / Briand, L. / Pernollet, J.-C. / Cambillau, C. / Tegoni, M.
CitationJournal: To be Published
Title: Conformational Changes of the Pheromone Binding Protein ASP1 from the Honeybee Apis mellifera L upon Ligand Binding
Authors: Pesenti, M.E. / Spinelli, S. / Briand, L. / Pernollet, J.-C. / Cambillau, C. / Tegoni, M.
History
DepositionJun 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6076
Polymers13,1951
Non-polymers4125
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.098, 85.997, 50.839
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-125-

HOH

21A-138-

HOH

DetailsThe biological assembly is the monomer

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Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13194.789 Da / Num. of mol.: 1 / Fragment: residues 26-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Production host: Pichia pastoris (fungus) / References: UniProt: Q9U9J6, UniProt: Q8WRW5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 200 nL of a 40 mg/mL protein solution in Tris 10 mM, NaCl 25 mM, mixed with 100 nL of 2.2 M ammonium sulfate, 0.2 M ammonium iodide, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2005
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 4835 / Num. obs: 4835 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.667 Å / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.86 / SU B: 21.587 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.623 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26625 755 14.1 %RANDOM
Rwork0.21034 ---
obs0.21818 4593 99.48 %-
all-4835 --
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: 72.486 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2---0.5 Å20 Å2
3----0.87 Å2
Refine analyzeLuzzati sigma a free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 23 16 946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022944
X-RAY DIFFRACTIONr_bond_other_d0.0020.02610
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9871285
X-RAY DIFFRACTIONr_angle_other_deg0.9543.0081501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61727.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59415156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.104152
X-RAY DIFFRACTIONr_chiral_restr0.0770.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
X-RAY DIFFRACTIONr_nbd_refined0.2380.2223
X-RAY DIFFRACTIONr_nbd_other0.1860.2572
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2467
X-RAY DIFFRACTIONr_nbtor_other0.0870.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1082750
X-RAY DIFFRACTIONr_mcbond_other0.5942233
X-RAY DIFFRACTIONr_mcangle_it2.8593950
X-RAY DIFFRACTIONr_scbond_it2.2972408
X-RAY DIFFRACTIONr_scangle_it2.8873335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 61 -
Rwork0.238 315 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.0751 Å / Origin y: 13.6597 Å / Origin z: -0.1999 Å
111213212223313233
T-0.4782 Å2-0.0502 Å20.0078 Å2--0.5564 Å20.0055 Å2---0.5142 Å2
L0.6782 °20.6749 °20.5889 °2-1.0666 °20.1903 °2--5.0469 °2
S0.2044 Å °-0.141 Å °0.1462 Å °0.1022 Å °-0.1305 Å °-0.2764 Å °-0.3327 Å °0.4056 Å °-0.0739 Å °

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