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- PDB-1eqk: SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHI... -

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Basic information

Entry
Database: PDB / ID: 1eqk
TitleSOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHIBITOR OF THE RICE, ORYZA SATIVA L. JAPONICA
ComponentsORYZACYSTATIN-I
KeywordsHYDROLASE INHIBITOR / alpha and beta proteins / cystatin-like fold / cystatin/monellin superfamily / phytocystatin family
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / defense response / extracellular region
Similarity search - Function
Aspartic acid proteinase inhibitor / Cystatin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Cysteine proteinase inhibitor 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsNagata, K. / Kudo, N. / Abe, K. / Arai, S. / Tanokura, M.
CitationJournal: Biochemistry / Year: 2000
Title: Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica.
Authors: Nagata, K. / Kudo, N. / Abe, K. / Arai, S. / Tanokura, M.
History
DepositionApr 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORYZACYSTATIN-I


Theoretical massNumber of molelcules
Total (without water)11,3991
Polymers11,3991
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)21 / 100structures with favorable non-bond energy
RepresentativeModel #21minimized average structure

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Components

#1: Protein ORYZACYSTATIN-I


Mass: 11398.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Species: Oryza sativa / Strain: Japonica Group / Tissue: SEED / Plasmid: PLASMID PET-26B(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P09229

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
132HNHA
NMR detailsText: The structure was determined using 1H and 15N NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM oryzacystatin-I; 50 mM sodium phosphate/100 mM NaCl/0.02% NaN3, pH 6.8; 10% D2O/90% H2O10% D2O/90% H2O
22 mM oryzacystatin-I U-15N; 50 mM sodium phosphate/100 mM NaCl/0.02% NaN3, pH 6.8; 10% D2O/90% H2O10% D2O/90% H2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3BVariancollection
NMRPipe1.6Delaglio, F. et al.processing
NMRDraw1.6Delaglio, F. et al.data analysis
Felix95Molecular Simulationsdata analysis
PIPP/CAPP4Garrett, D. et al.data analysis
DYANA1.4Guentert, P. et al.structure solution
CNS0.9Brunger,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
AQUA2Rullmann, J.A.C. et al.data analysis
PROCHECK-NMR3.4Laskowski, R.A. et al.data analysis
MOLMOL2.6Koradi, R. et al.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: A total of 1383 restraints, consisting of 1183 interproton distance restraints (338 long-range (|i - j| >= 6), 228 medium-range (2 <= |i - j| <= 5), 351 sequential (|i - j| = 1) and 266 intraresidual (|i - j| = 0)), 108 hydrogen bond restraints (representing 54 hydrogen bonds) and 92 torsion angle restraints (54 phi and 38 chi1), were used in the structure calculations by torsion angle dynamics using DYANA (ver. 1.4). A final set of 20 structures was selected from 100 calculations on the basis of agreement with the experimental data and van der Waals' energy. The average coordinates of the 20 DYANA structures were subjected to energy-minimization using CNS (ver. 0.9).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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