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- PDB-5v13: Mosquito juvenile hormone-binding protein -

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Basic information

Entry
Database: PDB / ID: 5v13
TitleMosquito juvenile hormone-binding protein
ComponentsAAEL008620-PA odorant-binding protein
KeywordsHormone-binding protein / Odorant-binding protein / Aedes / Anopheles / Culex / D7
Function / homology: / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / extracellular region / Chem-JH3 / Uncharacterized protein
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsAndersen, J.F. / Kim, I.H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A mosquito hemolymph odorant-binding protein family member specifically binds juvenile hormone.
Authors: Kim, I.H. / Pham, V. / Jablonka, W. / Goodman, W.G. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionMar 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: AAEL008620-PA odorant-binding protein
A: AAEL008620-PA odorant-binding protein
C: AAEL008620-PA odorant-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5316
Polymers98,7323
Non-polymers7993
Water11,872659
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-1 kcal/mol
Surface area34190 Å2
Unit cell
Length a, b, c (Å)120.150, 69.070, 121.940
Angle α, β, γ (deg.)90.000, 112.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AAEL008620-PA odorant-binding protein


Mass: 32910.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AaeL_AAEL008620, AAEL008620 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q16Y94
#2: Chemical ChemComp-JH3 / methyl (2E,6E)-9-[(2R)-3,3-dimethyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate / JH III / juvenile hormone III


Mass: 266.376 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H26O3 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.37 Å3/Da / Density % sol: 48.13 % / Description: Thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6, 30% PEG 6000, 3.5 % sorbitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2016 / Details: Si-111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.84→55.376 Å / Num. obs: 78904 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.84-1.883.520.5252.73199.8
1
1
1
1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å55.38 Å
Translation3.6 Å55.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→55.376 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 3720 4.9 %
Rwork0.1638 72247 -
obs0.1655 75967 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 25.9404 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.84→55.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 57 659 7242
Biso mean--18.22 33.09 -
Num. residues----803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076764
X-RAY DIFFRACTIONf_angle_d0.8289157
X-RAY DIFFRACTIONf_chiral_restr0.046927
X-RAY DIFFRACTIONf_plane_restr0.0051210
X-RAY DIFFRACTIONf_dihedral_angle_d17.4184051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86330.26491310.22752472260388
1.8633-1.88780.26411490.2132423257288
1.8878-1.91370.2551280.20362490261889
1.9137-1.94110.29651090.20322572268191
1.9411-1.970.22511590.19132590274992
1.97-2.00080.24491390.18432578271794
2.0008-2.03360.21581370.18182688282595
2.0336-2.06870.23411360.1922656279295
2.0687-2.10630.2391250.18292699282496
2.1063-2.14680.24061500.17432689283996
2.1468-2.19060.1981220.17172718284096
2.1906-2.23830.20751300.16962677280795
2.2383-2.29030.21581030.18092707281096
2.2903-2.34760.2051270.17622726285397
2.3476-2.41110.24531410.16752677281896
2.4111-2.4820.21721610.17552722288397
2.482-2.56220.22591570.16572725288297
2.5622-2.65370.18121390.17292724286397
2.6537-2.760.17641050.16052749285497
2.76-2.88560.20891660.16622692285896
2.8856-3.03770.18421480.17132728287698
3.0377-3.2280.1871580.16472727288597
3.228-3.47720.19361400.15382766290697
3.4772-3.82710.15921320.13992763289597
3.8271-4.38060.15821660.13072696286296
4.3806-5.51840.14491290.13152752288196
5.5184-55.40150.18931330.16492841297496
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)
10.5458-0.13340.16021.49720.45941.68060.0277-0.0472-0.0690.0062-0.0263-0.02710.03650.01130.01180.0636-0.00550.02560.09550.01990.1507234.8561-25.4287362.5019
21.08130.25-0.66220.9394-0.11631.68530.0011-0.04470.12030.01140.038-0.0603-0.01710.0574-0.02140.08460.0092-0.02630.0776-00.153253.24814.9021362.483
31.4608-0.42280.38260.953-0.51451.5670.02010.0514-0.07280.05590.01130.1649-0.0352-0.0414-0.01080.0973-0.00560.01890.0751-0.02510.1617217.61565.5925362.6516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 20 through 288)B20 - 288
2X-RAY DIFFRACTION2(chain 'A' and resid 20 through 288)A20 - 288
3X-RAY DIFFRACTION3(chain 'C' and resid 20 through 288)C20 - 288

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