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Yorodumi- PDB-2pre: Crystal structure of plant cysteine protease Ervatamin-C complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pre | ||||||
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Title | Crystal structure of plant cysteine protease Ervatamin-C complexed with irreversible inhibitor E-64 at 2.7 A resolution | ||||||
Components | Ervatamin-C | ||||||
Keywords | HYDROLASE / protease-inhibitor complex / papain-like fold / plant cysteine protease / Ervatamin | ||||||
Function / homology | Function and homology information cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases Similarity search - Function | ||||||
Biological species | Tabernaemontana divaricata (crepe jasmine) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ghosh, R. / Chakrabarti, C. / Dattagupta, J.K. / Biswas, S. | ||||||
Citation | Journal: Febs J. / Year: 2008 Title: Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria. Authors: Ghosh, R. / Chakraborty, S. / Chakrabarti, C. / Dattagupta, J.K. / Biswas, S. | ||||||
History |
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Remark 999 | SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pre.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pre.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2pre ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2pre | HTTPS FTP |
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-Related structure data
Related structure data | 3bcnC 2pnsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22994.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: tropical flowering plant Source: (natural) Tabernaemontana divaricata (crepe jasmine) References: UniProt: A8DS38, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: Precipitant solution - 0.2M Ammonium Sulphate and 30% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 2006 / Details: MAR CONFOCAL MULTILAYER OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 12883 / Num. obs: 12869 / % possible obs: 95.1 % / Redundancy: 3.36 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1258 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PNS Resolution: 2.7→14.94 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 865154.36 / Data cutoff high rms absF: 865154.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.2815 Å2 / ksol: 0.322029 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→14.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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