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- PDB-6qjb: Truncated Evasin-3 (tEv3 17-56) -

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Basic information

Entry
Database: PDB / ID: 6qjb
TitleTruncated Evasin-3 (tEv3 17-56)
ComponentsEvasin-3
KeywordsIMMUNE SYSTEM / chemokine-binding protein / ticks
Function / homologynegative regulation of protein homodimerization activity / negative regulation of chemokine activity / C-X-C chemokine binding / extracellular region / Evasin-3
Function and homology information
Biological speciesRhipicephalus sanguineus (brown dog tick)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDenisov, S.S. / Ippel, J.H. / Heinzman, A.C.A. / Koenen, R.R. / Ortega-Gomez, A. / Soehnlein, O. / Hackeng, T.M. / Dijkgraaf, I.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.013.009 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Tick saliva protein Evasin-3 modulates chemotaxis by disrupting CXCL8 interactions with glycosaminoglycans and CXCR2.
Authors: Denisov, S.S. / Ippel, J.H. / Heinzmann, A.C.A. / Koenen, R.R. / Ortega-Gomez, A. / Soehnlein, O. / Hackeng, T.M. / Dijkgraaf, I.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 17, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evasin-3


Theoretical massNumber of molelcules
Total (without water)4,3151
Polymers4,3151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3140 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Evasin-3


Mass: 4314.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rhipicephalus sanguineus (brown dog tick) / References: UniProt: P0C8E8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic13D HNCO
131anisotropic13D HN(CA)CB
141anisotropic13D CBCA(CO)NH
151anisotropic12D 1H-13C HSQC
161anisotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 100 mM EDTA, 200 mM sodium azide, 25 mM [U-2H] sodium acetate, 95% H2O/5% D2O
Label: tEv3 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMEDTAnatural abundance1
200 mMsodium azidenatural abundance1
25 mMsodium acetate[U-2H]1
Sample conditionsIonic strength: 325 mM / Label: 1 / pH: 4.5 / Pressure: 1 atm / Temperature: 37 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYBioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMReHyojung Ryu, GyuTae Lim, Bong Hyun Sung, Jinhyuk Leerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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