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Yorodumi- PDB-1eqk: SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eqk | ||||||
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Title | SOLUTION STRUCTURE OF ORYZACYSTATIN-I, A CYSTEINE PROTEINASE INHIBITOR OF THE RICE, ORYZA SATIVA L. JAPONICA | ||||||
Components | ORYZACYSTATIN-I | ||||||
Keywords | HYDROLASE 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 | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model type details | minimized average | ||||||
Authors | Nagata, K. / Kudo, N. / Abe, K. / Arai, S. / Tanokura, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqk.cif.gz | 657.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqk.ent.gz | 567.9 KB | Display | PDB format |
PDBx/mmJSON format | 1eqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqk ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using 1H and 15N NMR spectroscopy. |
-Sample preparation
Details |
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Sample conditions | pH: 6.8 / Pressure: ambient / Temperature: 298 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with favorable non-bond energy Conformers calculated total number: 100 / Conformers submitted total number: 21 |