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- PDB-8r6t: NMR solution structure of thyropin IrThy-Cd from the hard tick Ix... -

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Basic information

Entry
Database: PDB / ID: 8r6t
TitleNMR solution structure of thyropin IrThy-Cd from the hard tick Ixodes ricinus
ComponentsPutative two thyropin protein (Fragment)
KeywordsPROTEIN BINDING / STRUCTURE FROM CYANA 3.98.13
Function / homologyThyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Putative two thyropin protein
Function and homology information
Biological speciesIxodes ricinus (castor bean tick)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSrb, P. / Veverka, V. / Matouskova, Z. / Orsaghova, K. / Mares, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of Sciences Czech Republic
CitationJournal: Int J Mol Sci / Year: 2024
Title: An Unusual Two-Domain Thyropin from Tick Saliva: NMR Solution Structure and Highly Selective Inhibition of Cysteine Cathepsins Modulated by Glycosaminoglycans.
Authors: Matouskova, Z. / Orsaghova, K. / Srb, P. / Pytelkova, J. / Kukacka, Z. / Busa, M. / Hajdusek, O. / Sima, R. / Fabry, M. / Novak, P. / Horn, M. / Kopacek, P. / Mares, M.
History
DepositionNov 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative two thyropin protein (Fragment)


Theoretical massNumber of molelcules
Total (without water)7,8501
Polymers7,8501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Putative two thyropin protein (Fragment)


Mass: 7849.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A131Y7Z7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic13D 1H-15N NOESY
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] Tyropin, 100 mM sodium chloride, 25 mM TRIS, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMTyropin[U-13C; U-15N]1
100 mMsodium chloridenatural abundance1
25 mMTRISnatural abundance1
Sample conditionsIonic strength: 125 mM / Label: c1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYNMRFAM-SPARKYchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 30

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