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- PDB-2k2z: Solution structure of the folded domain of intermediate IIIb of T... -

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Basic information

Entry
Database: PDB / ID: 2k2z
TitleSolution structure of the folded domain of intermediate IIIb of Tick Carboxypeptidase Inhibitor
ComponentsCarboxypeptidase inhibitor
KeywordsHYDROLASE INHIBITOR / IIIB / Blood coagulation / Fibrinolysis / Metalloenzyme inhibitor / Metalloprotease inhibitor / Secreted
Function / homology
Function and homology information


acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / blood coagulation / toxin activity / extracellular region
Similarity search - Function
Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Myotoxin/Anemone neurotoxin domain superfamily
Similarity search - Domain/homology
Carboxypeptidase inhibitor
Similarity search - Component
Biological speciesRhipicephalus bursa (arthropod)
MethodSOLUTION NMR / simulated annealing
AuthorsPantoja-Uceda, D. / Blanco, F.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The NMR structures of the major intermediates of the two-domain tick carboxypeptidase inhibitor reveal symmetry in its folding and unfolding pathways.
Authors: Arolas, J.L. / Pantoja-Uceda, D. / Ventura, S. / Blanco, F.J. / Aviles, F.X.
History
DepositionApr 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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: Carboxypeptidase inhibitor


Theoretical massNumber of molelcules
Total (without water)4,1741
Polymers4,1741
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Carboxypeptidase inhibitor / TCI


Mass: 4173.843 Da / Num. of mol.: 1 / Fragment: UNP residues 59-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EPH2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.00 mM IIIB, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.00 mM / Component: IIIB
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: standard CYANA protocol of NOE assignment and structure calculation. The 20 conformers with the lowest final CYANA target function values were subject to restrained energy-minimization in ...Details: standard CYANA protocol of NOE assignment and structure calculation. The 20 conformers with the lowest final CYANA target function values were subject to restrained energy-minimization in explicit water using AMBER 9.0
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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