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- PDB-6hhe: Crystal structure of the medfly Odorant Binding Protein CcapOBP22... -

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Basic information

Entry
Database: PDB / ID: 6hhe
TitleCrystal structure of the medfly Odorant Binding Protein CcapOBP22/CcapOBP69a
ComponentsOdorant binding protein OBP69a
KeywordsTRANSPORT PROTEIN / Odorant Binding Proteins / OBP / pheromone / insect olfaction
Function / homology: / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Odorant binding protein OBP69a
Function and homology information
Biological speciesCeratitis capitata (Mediterranean fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.516 Å
AuthorsFalchetto, M. / Ciossani, G. / Nenci, S. / Mattevi, A. / Gasperi, G. / Forneris, F.
CitationJournal: Insect Mol.Biol. / Year: 2019
Title: Structural and biochemical evaluation of Ceratitis capitata odorant-binding protein 22 affinity for odorants involved in intersex communication.
Authors: Falchetto, M. / Ciossani, G. / Scolari, F. / Di Cosimo, A. / Nenci, S. / Field, L.M. / Mattevi, A. / Zhou, J.J. / Gasperi, G. / Forneris, F.
History
DepositionAug 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.title
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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: Odorant binding protein OBP69a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1454
Polymers13,8331
Non-polymers3123
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-26 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.030, 43.030, 136.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-203-

PG0

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Components

#1: Protein Odorant binding protein OBP69a


Mass: 13833.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceratitis capitata (Mediterranean fruit fly)
Gene: OBP69a / Plasmid: pJexpress414
Details (production host): N-terminal 8xHis + Prescission cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8W3V2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES pH 6.5, 1.6 M Ammonium Sulfate, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.516→43.03 Å / Num. obs: 20882 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Net I/σ(I): 16.7
Reflection shellResolution: 1.516→1.54 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.45 / Num. unique obs: 1017 / CC1/2: 0.924 / Rpim(I) all: 0.241 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OGN

3ogn


Resolution: 1.516→41.036 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 983 4.72 %
Rwork0.193 --
obs0.1944 20814 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.516→41.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 18 79 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015956
X-RAY DIFFRACTIONf_angle_d1.3271302
X-RAY DIFFRACTIONf_dihedral_angle_d16.373585
X-RAY DIFFRACTIONf_chiral_restr0.063157
X-RAY DIFFRACTIONf_plane_restr0.008165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.516-1.59590.26251240.22062782X-RAY DIFFRACTION100
1.5959-1.69590.22511600.20652730X-RAY DIFFRACTION100
1.6959-1.82690.2281490.20882763X-RAY DIFFRACTION100
1.8269-2.01070.22571170.19892818X-RAY DIFFRACTION100
2.0107-2.30170.22591510.18462808X-RAY DIFFRACTION100
2.3017-2.89970.19671460.19612869X-RAY DIFFRACTION100
2.8997-41.05070.22591360.18853061X-RAY DIFFRACTION100
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)
10.00240.0250.00020.1878-0.08250.0321-0.196-0.54690.26530.0783-0.5087-0.2981-0.0079-0.2393-0.04320.1302-0.0518-0.07490.5701-0.10540.222326.555712.2274-1.9754
20.02850.0516-0.01360.0653-0.0009-0.0105-0.3992-0.30030.5104-0.03460.1387-0.0132-0.145-0.18070.00090.12720.0363-0.03690.3476-0.020.254516.766516.3392-13.4372
30.59970.5148-0.30460.56520.06230.110.044-0.1064-0.16660.0197-0.1548-0.21280.02870.1925-0.02980.0950.00820.00790.35240.05350.209923.03622.5067-9.897
40.2608-0.3268-0.15620.1617-0.09440.1307-0.3509-0.1513-0.050.26050.1296-0.16210.36470.16340.00010.30320.0258-0.01480.19750.00470.207511.4249-5.50761.0731
50.12840.1823-0.47420.443-0.10920.46320.00150.08220.136-0.17940.0804-0.0717-0.0590.08850.00010.1644-0.0020.0470.24820.03520.224115.1483.2542-9.9818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 26 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 79 )
5X-RAY DIFFRACTION5chain 'A' and (resid 80 through 115 )

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