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- PDB-4z39: Structure of OBP3 from the vetch aphid Megoura viciae -

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Basic information

Entry
Database: PDB / ID: 4z39
TitleStructure of OBP3 from the vetch aphid Megoura viciae
ComponentsOdorant-binding protein
Keywordsodorant binding protein
Function / homologyPheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / extracellular space / membrane / Odorant binding protein 3 / Odorant-binding protein
Function and homology information
Biological speciesMegoura viciae (vetch aphid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsNorthey, T. / Venthur, H. / De Biasio, F. / Chauviac, F.-X. / Cole, A.R. / Field, L.M. / Zhou, J.-J. / Keep, N.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L001683/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/I024941/1 United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: Crystal Structures and Binding Dynamics of Odorant-Binding Protein 3 from two aphid species Megoura viciae and Nasonovia ribisnigri.
Authors: Northey, T. / Venthur, H. / De Biasio, F. / Chauviac, F.X. / Cole, A. / Ribeiro, K.A. / Grossi, G. / Falabella, P. / Field, L.M. / Keep, N.H. / Zhou, J.J.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 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: Odorant-binding protein
B: Odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6396
Polymers27,2632
Non-polymers3764
Water3,585199
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-31 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.220, 41.390, 44.310
Angle α, β, γ (deg.)100.28, 101.74, 105.03
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Odorant-binding protein


Mass: 13631.554 Da / Num. of mol.: 2 / Fragment: residues 24-141 / Mutation: ASM on N terminus from vector
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megoura viciae (vetch aphid) / Gene: OBP / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLyss / References: UniProt: B6E9V6, UniProt: A0A0S2E5N6*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.3 M AmSO4, 30% (w/v) PEG 4000, 7.5% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.3→38.76 Å / Num. obs: 52318 / % possible obs: 90.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fragments

Resolution: 1.3→38.76 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.842 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16115 2615 5 %RANDOM
Rwork0.12463 ---
obs0.12649 49540 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20.19 Å20.58 Å2
2--0.04 Å2-0.68 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.3→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 22 199 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022010
X-RAY DIFFRACTIONr_bond_other_d0.0110.021891
X-RAY DIFFRACTIONr_angle_refined_deg2.781.9872726
X-RAY DIFFRACTIONr_angle_other_deg1.9843.0034416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9245.037267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71226.62377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82915398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.665152
X-RAY DIFFRACTIONr_chiral_restr0.1950.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022228
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02394
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2791.931995
X-RAY DIFFRACTIONr_mcbond_other2.1121.924994
X-RAY DIFFRACTIONr_mcangle_it2.6682.91248
X-RAY DIFFRACTIONr_mcangle_other2.6672.9051249
X-RAY DIFFRACTIONr_scbond_it5.272.5221015
X-RAY DIFFRACTIONr_scbond_other5.272.5221015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5583.5811467
X-RAY DIFFRACTIONr_long_range_B_refined4.5717.6482637
X-RAY DIFFRACTIONr_long_range_B_other4.56917.6572638
X-RAY DIFFRACTIONr_rigid_bond_restr5.9733901
X-RAY DIFFRACTIONr_sphericity_free22.938572
X-RAY DIFFRACTIONr_sphericity_bonded11.48453986
Refine LS restraints NCS

Ens-ID: 1 / Number: 13298 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 173 -
Rwork0.256 3375 -
obs--82.11 %

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