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- PDB-2jzm: Chymotrypsin inhibitor C1 from Nicotiana alata -

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Basic information

Entry
Database: PDB / ID: 2jzm
TitleChymotrypsin inhibitor C1 from Nicotiana alata
ComponentsProteinase inhibitor
KeywordsHYDROLASE INHIBITOR / protein / proteinase inhibitor / chymotrypsin inhibitor / plant / insecticidal
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
Similarity search - Function
Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteinase inhibitor / Proteinase inhibitor
Similarity search - Component
Biological speciesNicotiana alata (Persian tobacco)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsrefined structure
AuthorsSchirra, H.J. / Anderson, M.A. / Craik, D.J.
Citation
Journal: Protein Pept.Lett. / Year: 2008
Title: Structural refinement of insecticidal plant proteinase inhibitors from Nicotiana alata.
Authors: Schirra, H.J. / Anderson, M.A. / Craik, D.J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The three-dimensional solution structure by 1H NMR of a 6-kDa proteinase inhibitor isolated from the stigma of Nicotiana alata.
Authors: Nielsen, K.J. / Heath, R.L. / Anderson, M.A. / Craik, D.J.
History
DepositionJan 9, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / pdbx_nmr_sample_details ...citation / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_DOI / _pdbx_nmr_sample_details.contents
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)5,7461
Polymers5,7461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Proteinase inhibitor


Mass: 5746.476 Da / Num. of mol.: 1 / Fragment: residues 1-53 (UNP residues 54-106) / Source method: isolated from a natural source / Source: (natural) Nicotiana alata (Persian tobacco) / References: UniProt: Q9SQ77, UniProt: Q40378*PLUS
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM C1, 90% H2O/10% D2O90% H2O/10% D2O
2100% D2O100% D2O
SampleConc.: 1.2 mM / Component: C1
Sample conditionsIonic strength: 0 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRBruker Biospincollection
UXNMRBruker Biospinprocessing
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges, Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: MEthod followed the protocol of Linge et al., Proteins 50, 496 (2003) with the modifications in Nederveen et al., Proteins 59, 662 (2005), as above
NMR constraintsNOE constraints total: 538 / NOE intraresidue total count: 291 / NOE long range total count: 55 / NOE medium range total count: 22 / NOE sequential total count: 120 / Protein chi angle constraints total count: 18 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 26 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Torsion angle constraint violation method: cns_solve
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.002 Å

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