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- PDB-2kcr: Solution structure of anntoxin -

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Basic information

Entry
Database: PDB / ID: 2kcr
TitleSolution structure of anntoxin
Componentsanntoxin
KeywordsTOXIN / Protein
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Function and homology information
Biological speciesHyla annectans (Assam treefrog)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsHong, J. / You, D. / Lai, R. / Lin, D.
CitationJournal: To be Published
Title: Solution structure of anntoxin
Authors: Hong, J. / You, D. / Lai, R. / Lin, D.
History
DepositionDec 29, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
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: anntoxin


Theoretical massNumber of molelcules
Total (without water)6,8341
Polymers6,8341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein anntoxin


Mass: 6834.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyla annectans (Assam treefrog) / Plasmid: PET32a+ / Production host: Escherichia coli (E. coli)
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: kunitz type
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM protein-1, 90% H2O-2, 10% [U-2H] D2O-3, 90% H2O/10% D2O90% H2O/10% D2O
22mM protein-4, 100% [U-2H] D2O-5, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMprotein-11
90 %H2O-21
10 %D2O-3[U-2H]1
2 mMprotein-42
100 %D2O-5[U-2H]2
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue, Nilgeschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges, Readstructure solution
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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