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- PDB-6mt7: Phlebotomus duboscqi salivary D7 protein, selenomethionine derivative -

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Basic information

Entry
Database: PDB / ID: 6mt7
TitlePhlebotomus duboscqi salivary D7 protein, selenomethionine derivative
Components26.7 kDa salivary protein
KeywordsLIPID BINDING PROTEIN / odorant-binding protein / leukotriene / thromboxane
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 / SAD / Resolution: 1.78 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 1.1Oct 30, 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

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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)54,6384
Polymers53,9332
Non-polymers7052
Water9,170509
1
A: 26.7 kDa salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3192
Polymers26,9671
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)27,3192
Polymers26,9671
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.908, 101.515, 33.539
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: 26966.619 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.: 509 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 6000m 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97499 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97499 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 90692 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Χ2: 1.604 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.40.19444860.9530.1180.2290.82798.7
1.81-1.844.10.17245330.9730.0930.1970.87699.2
1.84-1.884.40.16444750.9780.0840.1850.94199
1.88-1.924.50.14144600.9820.0720.1590.94399.3
1.92-1.964.50.12546030.9850.0640.1410.99199.5
1.96-24.50.11344830.9880.0570.1271.05299.7
2-2.054.50.09745270.990.0490.1091.10199.7
2.05-2.114.50.08745750.9930.0450.0981.16599.7
2.11-2.174.60.08245010.9920.0410.0921.26599.8
2.17-2.244.60.0846050.9930.0410.091.499.9
2.24-2.324.60.0844890.9930.0410.091.53699.9
2.32-2.424.60.07845900.9930.040.0881.759100
2.42-2.534.60.07845000.9930.040.0881.96100
2.53-2.664.70.07445320.9930.0380.0832.038100
2.66-2.834.70.06545770.9950.0330.0731.914100
2.83-3.044.80.05745770.9960.0290.0641.892100
3.04-3.354.80.05845370.9950.030.0662.365100
3.35-3.834.70.05645120.9960.0290.0632.898100
3.83-4.834.80.04745900.9970.0240.0522.445100
4.83-104.80.04345400.9980.0220.0492.03299.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→43.371 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.34 / Phase error: 19.22
RfactorNum. reflection% reflection
Rfree0.2062 4492 4.96 %
Rwork0.1683 --
obs0.1702 90597 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 17.3937 Å2 / Biso min: 5.43 Å2
Refinement stepCycle: final / Resolution: 1.78→43.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 50 509 4305
Biso mean--18.36 27.22 -
Num. residues----460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7803-1.80050.27971540.22462750290498
1.8005-1.82170.2851500.21582818296899
1.8217-1.84390.27241300.18932967309799
1.8439-1.86720.22881560.19042887304399
1.8672-1.89180.20341530.16282774292799
1.8918-1.91770.20511400.16812830297099
1.9177-1.94510.21831370.17729403077100
1.9451-1.97410.24231390.182429093048100
1.9741-2.0050.20751410.186828232964100
2.005-2.03790.22491240.174428843008100
2.0379-2.0730.25731430.177229063049100
2.073-2.11070.1991870.172228673054100
2.1107-2.15130.26311350.172728202955100
2.1513-2.19520.19351250.163529053030100
2.1952-2.24290.21850.166729333118100
2.2429-2.29510.21761940.171627672961100
2.2951-2.35250.22161330.171628883021100
2.3525-2.41610.22011490.174829453094100
2.4161-2.48720.21791640.171728322996100
2.4872-2.56750.16261410.164729013042100
2.5675-2.65920.20631370.168828612998100
2.6592-2.76570.22691810.166328983079100
2.7657-2.89150.18341670.168928363003100
2.8915-3.04390.18281900.163728723062100
3.0439-3.23460.23871310.167528492980100
3.2346-3.48420.22811440.164829023046100
3.4842-3.83470.19461400.151328843024100
3.8347-4.38910.16991260.143628913017100
4.3891-5.5280.16421320.15629363068100
5.528-43.38380.17411640.17692830299499
Refinement TLS params.Method: refined / Origin x: 35.3196 Å / Origin y: 2.6787 Å / Origin z: 0.7016 Å
111213212223313233
T0.0995 Å2-0.0159 Å20.0036 Å2-0.0712 Å20.0193 Å2--0.0751 Å2
L0.7816 °2-0.3323 °20.2492 °2--0.0043 °2-0.0437 °2--0.1734 °2
S-0.0312 Å °0.0062 Å °0.0414 Å °0.025 Å °0.0098 Å °-0.0186 Å °-0.0131 Å °0.0204 Å °0.0207 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 230
2X-RAY DIFFRACTION1allB0 - 230
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allF1 - 510

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