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- PDB-2n17: NMR structure of a Kazal-type serine protease inhibitor from the ... -

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Basic information

Entry
Database: PDB / ID: 2n17
TitleNMR structure of a Kazal-type serine protease inhibitor from the subterranean termite defense gland of Coptotermes formosanus Shiraki soldiers
ComponentsLysozyme-Protease Inhibitor Protein
KeywordsHYDROLASE / Kazal-type / serine protease inhibitor / chymotrypsin / elastase / termite / soldier / defense gland / secretion
Function / homologyKazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta / Lysozyme-Protease Inhibitor Protein
Function and homology information
Biological speciesCoptotermes formosanus (Formosan subterranean termite)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsNegulescu, H. / Guo, Y. / Garner, T.P. / Goodwin, O.Y. / Henderson, G. / Laine, R.A. / Macnaughtan, M.A.
CitationJournal: Plos One / Year: 2015
Title: A Kazal-Type Serine Protease Inhibitor from the Defense Gland Secretion of the Subterranean Termite Coptotermes formosanus Shiraki.
Authors: Negulescu, H. / Guo, Y. / Garner, T.P. / Goodwin, O.Y. / Henderson, G. / Laine, R.A. / Macnaughtan, M.A.
History
DepositionMar 23, 2015Deposition site: BMRB / Processing site: RCSB
SupersessionMay 6, 2015ID: 2M25
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme-Protease Inhibitor Protein


Theoretical massNumber of molelcules
Total (without water)8,5791
Polymers8,5791
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysozyme-Protease Inhibitor Protein


Mass: 8578.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptotermes formosanus (Formosan subterranean termite)
Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: V9GZ93
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-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1512D 1H-1H COSY
1613D 1H-15N NOESY
1713D 1H-15N TOCSY
1813D HN(CA)CB
1913D HN(COCA)CB
11013D HNCO
11113D HCACO
11213D 1H-13C NOESY
11313D (H)CCH-TOCSY
11413D HNHB

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] TFP4, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: TFP4-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VS 700 / Manufacturer: Varian / Model: VS 700 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJAgilentcollection
NMRPipe7.8Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPNMR2.2.2CCPNdata analysis
CCPNMR2.2.2CCPNpeak picking
CCPNMR2.2.2CCPNchemical shift assignment
CCPNMR2.2.2CCPNnoe assignment
CCPNMR2.2.2CCPNdihedral angle
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdihedral angle
PSVS1.5Bhattacharya and Montelionestructure validation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 526 / NOE intraresidue total count: 191 / NOE long range total count: 100 / NOE medium range total count: 50 / NOE sequential total count: 185
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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