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- PDB-4z45: Structure of OBP3 from the currant-lettuce aphid Nasonovia ribisnigri -

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Basic information

Entry
Database: PDB / ID: 4z45
TitleStructure of OBP3 from the currant-lettuce aphid Nasonovia ribisnigri
ComponentsOdorant-binding protein NribOBP3
Keywordsodorant binding protein
Function / homologyPheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Odorant-binding protein 3 / Odorant-binding protein NribOBP3
Function and homology information
Biological speciesNasonovia ribisnigri (lettuce aphid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 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
DepositionApr 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant-binding protein NribOBP3
B: Odorant-binding protein NribOBP3
D: Odorant-binding protein NribOBP3


Theoretical massNumber of molelcules
Total (without water)40,9373
Polymers40,9373
Non-polymers00
Water6,593366
1
A: Odorant-binding protein NribOBP3


Theoretical massNumber of molelcules
Total (without water)13,6461
Polymers13,6461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Odorant-binding protein NribOBP3


Theoretical massNumber of molelcules
Total (without water)13,6461
Polymers13,6461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Odorant-binding protein NribOBP3


Theoretical massNumber of molelcules
Total (without water)13,6461
Polymers13,6461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.250, 87.250, 95.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13B
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 116
2010B1 - 116
1020A1 - 118
2020D1 - 118
1030B1 - 116
2030D1 - 116

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Odorant-binding protein NribOBP3


Mass: 13645.580 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nasonovia ribisnigri (lettuce aphid) / Gene: obp3 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: C5J8G4, UniProt: A0A0M4AUH6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.1 M Sodium Citrate pH 5 10mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.02→59.16 Å / Num. obs: 27953 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.5
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.02→59.16 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.211 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20743 1402 5 %RANDOM
Rwork0.16359 ---
obs0.16576 26520 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å2-0 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.02→59.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 0 366 3133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022887
X-RAY DIFFRACTIONr_bond_other_d0.0140.022720
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.9743917
X-RAY DIFFRACTIONr_angle_other_deg1.9693.0026336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.465.053377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05526.581117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33215562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.3153
X-RAY DIFFRACTIONr_chiral_restr0.1270.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023213
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02578
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_it1.5321.6151435
X-RAY DIFFRACTIONr_mcbond_other1.5311.6131434
X-RAY DIFFRACTIONr_mcangle_it2.3532.3971795
X-RAY DIFFRACTIONr_mcangle_other2.3532.3991796
X-RAY DIFFRACTIONr_scbond_it2.6781.9651452
X-RAY DIFFRACTIONr_scbond_other2.6711.9611450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1552.8152109
X-RAY DIFFRACTIONr_long_range_B_refined6.77714.5373842
X-RAY DIFFRACTIONr_long_range_B_other6.44413.7543652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A135520.09
12B135520.09
21A135400.11
22D135400.11
31B134580.11
32D134580.11
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 110 -
Rwork0.194 1946 -
obs--100 %
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)
10.31110.31530.19420.5678-0.10390.7217-0.0198-0.0115-0.0169-0.0679-0.01220.0146-0.0240.04720.03190.0668-0.0257-0.00610.0504-0.00430.052414.0365-22.49181.1202
20.97550.52570.06751.1179-0.12160.0349-0.0022-0.1064-0.0709-0.02120.0065-0.01520.0043-0.0209-0.00430.0604-0.02840.02490.0341-0.01960.0746-4.7174-45.22164.0318
31.49980.712-0.60411.0805-0.11770.28320.1684-0.15670.0640.1065-0.14440.033-0.050.0414-0.0240.126-0.07960.01660.06-0.01320.003936.0679-51.84110.9544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 118
2X-RAY DIFFRACTION2B1 - 118
3X-RAY DIFFRACTION3D1 - 118

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