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- PDB-2jxd: NMR structure of human Serine protease inhibitor Kazal type II (S... -

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Basic information

Entry
Database: PDB / ID: 2jxd
TitleNMR structure of human Serine protease inhibitor Kazal type II (SPINK2)
ComponentsSerine protease inhibitor Kazal-type 2
KeywordsHYDROLASE INHIBITOR / anti-parallel beta sheet / beta-bulge / disulfide bond / alpha helix / Protease inhibitor / Pyrrolidone carboxylic acid / Secreted / Serine protease inhibitor
Function / homology
Function and homology information


acrosome assembly / endopeptidase inhibitor activity / spermatid development / acrosomal vesicle / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Serine protease inhibitor Kazal-type 2 / Kazal serine protease inhibitors family signature. / 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
Serine protease inhibitor Kazal-type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, Water refinement
AuthorsChen, T. / Lee, T.-R. / Lyu, P.-C.
CitationJournal: Proteins / Year: 2009
Title: Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor
Authors: Chen, T. / Lee, T.-R. / Liang, W.-G. / Chang, W.-S.W. / Lyu, P.-C.
History
DepositionNov 15, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 18, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease inhibitor Kazal-type 2


Theoretical massNumber of molelcules
Total (without water)7,0191
Polymers7,0191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine protease inhibitor Kazal-type 2 / Acrosin-trypsin inhibitor / HUSI-II


Mass: 7019.129 Da / Num. of mol.: 1 / Fragment: Kazal-type domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20155

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 1.5 mM SPINK2, 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: SPINK2
Sample conditionspH: 3.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger A.T. / Classification: refinement
RefinementMethod: simulated annealing, Water refinement / Software ordinal: 1
Details: Structure calculations were carried out with the standard simulated annealing protocol by using the CNS 1.1 program. Several rounds of calculations were used to eliminate the ambiguity in ...Details: Structure calculations were carried out with the standard simulated annealing protocol by using the CNS 1.1 program. Several rounds of calculations were used to eliminate the ambiguity in the assignment.Final structures were refined by the explicit water model using the OPLS force field in RECOORD and evaluated with PROCHECK-nmr.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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