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- PDB-6mtf: D7 protein from Phlebotomus duboscqi, native -

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Basic information

Entry
Database: PDB / ID: 6mtf
TitleD7 protein from Phlebotomus duboscqi, native
Components26.7 kDa salivary protein
KeywordsTRANSPORT PROTEIN / sand fly / odorant-binding protein / leukotriene / thromboxane / salivary
Function / homologyPheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / toxin activity / extracellular space / Long form salivary protein D7L
Function and homology information
Biological speciesPhlebotomus duboscqi (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsAndersen, J.F. / Jablonka, W.
CitationJournal: Sci Rep / Year: 2019
Title: Functional and structural similarities of D7 proteins in the independently-evolved salivary secretions of sand flies and mosquitoes.
Authors: Jablonka, W. / Kim, I.H. / Alvarenga, P.H. / Valenzuela, J.G. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: 26.7 kDa salivary protein
B: 26.7 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3574
Polymers53,6522
Non-polymers7052
Water8,467470
1
A: 26.7 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1782
Polymers26,8261
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 26.7 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1782
Polymers26,8261
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.890, 101.560, 33.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 26.7 kDa salivary protein


Mass: 26825.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebotomus duboscqi (insect) / Gene: M01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q06KA2
#2: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 6000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.92→41.487 Å / Num. obs: 38751 / % possible obs: 99.9 % / Redundancy: 11.85 % / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.2
Reflection shellResolution: 1.92→1.96 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 6.33 / Num. unique obs: 2811 / CC1/2: 0.927 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→41.487 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 18.11
RfactorNum. reflection% reflection
Rfree0.2084 1905 5.01 %
Rwork0.1637 --
obs0.1659 38058 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.34 Å2 / Biso mean: 18.534 Å2 / Biso min: 5.33 Å2
Refinement stepCycle: final / Resolution: 1.92→41.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 50 470 4266
Biso mean--20.03 26.58 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.96810.22981420.18212411255393
1.9681-2.02130.21571270.16932441256896
2.0213-2.08070.23771420.1592527266997
2.0807-2.14790.26531250.15992517264298
2.1479-2.22470.19351230.15452578270199
2.2247-2.31370.20311380.16192531266999
2.3137-2.4190.22441150.16082614272999
2.419-2.54650.20641330.16372561269499
2.5465-2.70610.20981370.17012573271099
2.7061-2.9150.21971610.16922565272699
2.915-3.20820.20281320.169126512783100
3.2082-3.67220.19971420.164226672809100
3.6722-4.62560.17461390.144726862825100
4.6256-41.49660.21481490.1762831298099
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)
11.0853-0.1102-0.02991.86260.04370.5898-0.02770.0013-0.08310.05070.0093-0.16010.04460.0360.01480.0755-0.01570.00430.09350.01640.064517.67025.1589-6.4648
21.09150.3694-0.22121.64720.07450.4059-0.01450.02360.1776-0.02020.02940.1638-0.08780.0008-0.0040.08930.007-0.02510.11950.01270.079153.4770.37977.9903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 230)A0 - 230
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 230)B0 - 230

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