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- PDB-2m5x: Novel method of protein purification for structural research. Exa... -

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Basic information

Entry
Database: PDB / ID: 2m5x
TitleNovel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.
ComponentsSilk protease inhibitor 2
KeywordsHYDROLASE inhibitor / serine protease inhibitor / Kazal family / SPI-2
Function / homology
Function and homology information


Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Silk protease inhibitor 2
Similarity search - Component
Biological speciesGalleria mellonella (greater wax moth)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsLenarcic Zivkovic, M. / Dvornyk, A. / Kludkiewicz, B. / Kopera, E. / Zagorski-Ostoja, W. / Grzelak, K. / Zhukov, I. / Bal, W.
CitationJournal: Plos One / Year: 2014
Title: Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor.
Authors: Kopera, E. / Bal, W. / Lenarcic Zivkovic, M. / Dvornyk, A. / Kludkiewicz, B. / Grzelak, K. / Zhukov, I. / Zagorski-Ostoja, W. / Jaskolski, M. / Krzywda, S.
History
DepositionMar 12, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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: Silk protease inhibitor 2


Theoretical massNumber of molelcules
Total (without water)4,3181
Polymers4,3181
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)17 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Silk protease inhibitor 2


Mass: 4317.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Galleria mellonella (greater wax moth) / Production host: Pichia pastoris (fungus) / References: UniProt: Q968S7
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 TOCSY
1212D 1H-1H NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 0.5 mM GmSPI 2, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: GmSPI 2-1
Sample conditionsIonic strength: 50 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 800 MHz

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Processing

NMR softwareName: CNS / Version: 1.3 / Developer: BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ / Classification: refinement
RefinementMethod: molecular 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: 17

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