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- PDB-2jto: Solution Structure of Tick Carboxypeptidase Inhibitor -

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Basic information

Entry
Database: PDB / ID: 2jto
TitleSolution Structure of Tick Carboxypeptidase Inhibitor
ComponentsCarboxypeptidase inhibitor
KeywordsHYDROLASE INHIBITOR / PROTEIN / 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 / toxin activity / extracellular region
Similarity search - Function
Carboxypeptidase inhibitor, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / ligand-binding face of the semaphorins, domain 2 / Single Sheet / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase inhibitor
Similarity search - Component
Biological speciesRhipicephalus bursa (arthropod)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPantoja-Uceda, D. / Blanco, F.J.
CitationJournal: Biochemistry / Year: 2008
Title: The NMR structure and dynamics of the two-domain tick carboxypeptidase inhibitor reveal flexibility in its free form and stiffness upon binding to human carboxypeptidase B.
Authors: Pantoja-Uceda, D. / Arolas, J.L. / Garcia, P. / Lopez-Hernandez, E. / Padro, D. / Aviles, F.X. / Blanco, F.J.
History
DepositionAug 3, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 9, 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

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Assembly

Deposited unit
A: Carboxypeptidase inhibitor


Theoretical massNumber of molelcules
Total (without water)7,9451
Polymers7,9451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Carboxypeptidase inhibitor / TCI


Mass: 7945.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EPH2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1422D 1H-15N HSQC
1523D 1H-15N NOESY
1623D 1H-15N TOCSY
1722D 1H-1H NOESY
1822D 1H-1H TOCSY
1922D 1H-15N HSQC
11023D HNHA
11123D HNHB
11232D 1H-15N HSQC
11332D 1H-13C HSQC
11433D HNCO
11533D CBCA(CO)NH
11633D HN(CA)CB
11733D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.76 mM [U-100% 15N] TCI, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-100% 15N] TCI, 95% H2O/5% D2O95% H2O/5% D2O
30.1 mM [U-100% 13C; U-100% 15N] TCI, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.76 mMTCI[U-100% 15N]1
0.7 mMTCI[U-100% 15N]2
0.1 mMTCI[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 78.4 / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MARSJung adn Markus Zweckstetterchemical shift calculation
GARANTBartels, Guntert, Billeter and Wuthrichchemical shift calculation
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
VADARDS Wishartdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: stucture calculation with torsion angel dynamics, the 20 conformers with the lowest final CYANA target were subjected to restrained energy minimization energy in vacuo with the program AMBER7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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