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- PDB-7tvy: Short form D7 protein from Culex quinquefasciatus -

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Basic information

Entry
Database: PDB / ID: 7tvy
TitleShort form D7 protein from Culex quinquefasciatus
ComponentsSalivary short D7 protein 3
KeywordsBLOOD CLOTTING / odorant-binding
Function / homologyPheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Putative salivary short D7 protein 3
Function and homology information
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsAndersen, J.F. / Alvarenga, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2022
Title: Functional aspects of evolution in a cluster of salivary protein genes from mosquitoes.
Authors: Alvarenga, P.H. / Dias, D.R. / Xu, X. / Francischetti, I.M.B. / Gittis, A.G. / Arp, G. / Garboczi, D.N. / Ribeiro, J.M.C. / Andersen, J.F.
History
DepositionFeb 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Salivary short D7 protein 3
B: Salivary short D7 protein 3
C: Salivary short D7 protein 3
D: Salivary short D7 protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4137
Polymers67,1254
Non-polymers2883
Water8,917495
1
A: Salivary short D7 protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,7811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Salivary short D7 protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,7811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Salivary short D7 protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,7811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Salivary short D7 protein 3


Theoretical massNumber of molelcules
Total (without water)16,7811
Polymers16,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.231, 122.809, 74.433
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Salivary short D7 protein 3


Mass: 16781.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q6TS00
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 5000 MME, 0.2 M lithium sulfate, 0.1 M Tris HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jan 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 41251 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.254 / Net I/σ(I): 13 / Num. measured all: 202477
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.98-2.013.50.42118221.097189.2
2.01-2.0540.37820971.076199.4
2.05-2.094.50.33820551.095199.7
2.09-2.134.90.30520371.111100
2.13-2.1850.25920761.131100
2.18-2.2350.23421021.191100
2.23-2.295.10.21220191.1341100
2.29-2.355.10.17720891.1511100
2.35-2.425.10.14820731.1881100
2.42-2.495.10.13620731.1751100
2.49-2.585.10.12220841.1871100
2.58-2.695.10.10620571.2471100
2.69-2.815.10.08120751.2851100
2.81-2.965.10.06720731.341100
2.96-3.145.10.05720631.3841100
3.14-3.395.10.04421041.4151100
3.39-3.735.10.03520861.3991100
3.73-4.265.10.03120671.4521100
4.26-5.3750.02920871.3831100
5.37-504.80.02921121.504199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å33.23 Å
Translation3.6 Å33.23 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 model

Resolution: 1.98→33.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 2070 5.02 %
Rwork0.1918 39143 -
obs0.1944 41213 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.3 Å2 / Biso mean: 31.747 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 1.98→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 15 495 4913
Biso mean--36.19 33.62 -
Num. residues----549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.030.31371120.26062490260295
2.03-2.080.31261490.237526502799100
2.08-2.130.27611560.219425312687100
2.13-2.20.27411360.206526502786100
2.2-2.270.2471370.214225962733100
2.27-2.350.28521350.203826072742100
2.35-2.440.2741390.20725882727100
2.44-2.550.30681260.214226932819100
2.55-2.690.28091200.219825782698100
2.69-2.860.2481440.203326072751100
2.86-3.080.30911650.209626012766100
3.08-3.390.22931300.189126562786100
3.39-3.880.18331260.16626232749100
3.88-4.880.1891320.152326452777100
4.88-33.230.20831630.17772628279199
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)
13.16960.4487-1.49074.6509-0.54842.2273-0.05790.0343-0.0338-0.1151-0.05910.04010.09460.05090.09580.1758-0.0294-0.0650.14540.00680.07754.07610.12828.4333
22.25680.90980.82232.91810.64953.52130.03910.06080.17680.0147-0.0251-0.2387-0.0663-0.0399-0.01550.10860.02130.0430.11920.01550.2045-7.9754-31.25731.793
33.0149-0.3412-0.93082.41460.21142.45760.0668-0.00570.0477-0.0787-0.0011-0.15240.11880.1948-0.05060.09680.0214-0.02270.17790.04020.1346-9.886510.4133-3.0942
41.4804-0.7586-0.44953.53750.37591.76090.41620.5592-0.1187-0.84-0.86690.3461-0.2499-0.4315-0.12030.40870.1932-0.03230.3899-0.10530.312110.7522-19.5044-7.5918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 138)A1 - 138
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 139)B1 - 139
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 138)C1 - 138
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 137)D1 - 137

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