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- PDB-7tvc: Short form D7 protein from Aedes aegypti -

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Basic information

Entry
Database: PDB / ID: 7tvc
TitleShort form D7 protein from Aedes aegypti
ComponentsSalivary short D7 protein
KeywordsBLOOD CLOTTING / odorant-binding
Function / homologyPheromone/general odorant binding protein domain / Pheromone/general odorant binding protein superfamily / odorant binding / Recoverin; domain 1 / Orthogonal Bundle / extracellular region / Mainly Alpha / Short form salivary protein D7S1
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.19 Å
AuthorsAndersen, J.F. / Xu, X.
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 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Salivary short D7 protein
A: Salivary short D7 protein


Theoretical massNumber of molelcules
Total (without water)28,9732
Polymers28,9732
Non-polymers00
Water7,602422
1
B: Salivary short D7 protein


Theoretical massNumber of molelcules
Total (without water)14,4871
Polymers14,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Salivary short D7 protein


Theoretical massNumber of molelcules
Total (without water)14,4871
Polymers14,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.653, 85.653, 30.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Salivary short D7 protein / 14.5 kDa secreted protein / 16.9 kDa secreted protein


Mass: 14486.610 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: SG14.5sp / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T9T4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 6000, 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→30.28 Å / Num. obs: 72163 / % possible obs: 99.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.2
Reflection shellResolution: 1.19→1.21 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 3265

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.19→30.28 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 3646 5.05 %
Rwork0.158 68517 -
obs0.1587 72163 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.84 Å2 / Biso mean: 13.4139 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: final / Resolution: 1.19→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 422 2418
Biso mean---23.37 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.19-1.20.2451090.23782362247191
1.2-1.220.21581260.22272510263696
1.22-1.240.22451390.19682620275998
1.24-1.260.1921150.18682613272899
1.26-1.280.19291350.179226412776100
1.28-1.30.23051510.179926282779100
1.3-1.320.1851370.174926592796100
1.32-1.340.18711350.176426512786100
1.34-1.370.17781410.169925842725100
1.37-1.40.18741420.159126602802100
1.4-1.430.18621580.158526142772100
1.43-1.460.16091530.149426192772100
1.46-1.50.16411450.14526362781100
1.5-1.540.1661360.143226732809100
1.54-1.580.15461370.145126272764100
1.58-1.630.14781390.140626502789100
1.63-1.690.14011370.140826292766100
1.69-1.760.1921360.148526642800100
1.76-1.840.16991590.153826292788100
1.84-1.940.18751490.152926842833100
1.94-2.060.17731520.15126412793100
2.06-2.220.15771420.152426652807100
2.22-2.440.15351450.150826522797100
2.44-2.790.16651380.159527012839100
2.79-3.520.15461410.155727142855100
3.52-30.280.17221490.159827912940100
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)
11.0828-0.3082-0.04581.25730.09660.6725-0.0237-0.0376-0.044-0.01920.0184-0.0026-0.00870.04030.00510.0463-0.00320.00230.04880.0120.042620.45795.7432-2.5322
21.0173-0.5520.13471.429-0.33620.6681-0.007-0.01610.0041-0.02530.0026-0.00340.0125-0.04340.00380.0574-0.0058-0.00390.0617-0.0140.054922.254338.0004-3.2566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 1 through 126)B1 - 126
2X-RAY DIFFRACTION2(chain 'A' and resid 1 through 126)A1 - 126

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