+Open data
-Basic information
Entry | Database: PDB / ID: 3ima | ||||||
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Title | Complex structure of tarocystatin and papain | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / CYSTATIN / TAROCYSTATIN / CECPI / PAPAIN / PHYTOCYSTATIN / Allergen / Disulfide bond / Hydrolase / Protease / Thiol protease / Zymogen / Protease inhibitor / Thiol protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information papain / cysteine-type endopeptidase inhibitor activity / serpin family protein binding / cysteine-type peptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Colocasia esculenta (taro) Carica papaya (papaya) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Chu, M.H. / Liu, K.L. / Yeh, K.W. / Cheng, Y.S. | ||||||
Citation | Journal: Planta / Year: 2011 Title: Crystal structure of tarocystatin-papain complex: implications for the inhibition property of group-2 phytocystatins. Authors: Chu, M.H. / Liu, K.L. / Wu, H.Y. / Yeh, K.W. / Cheng, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ima.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ima.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ima.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/3ima ftp://data.pdbj.org/pub/pdb/validation_reports/im/3ima | HTTPS FTP |
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-Related structure data
Related structure data | 3lfyC 1ppnS 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: 23500.299 Da / Num. of mol.: 2 / Fragment: Papain domain / Source method: isolated from a natural source Details: Papain was purchased from SIGMA co. for co-crystallization with CECPI. Source: (natural) Carica papaya (papaya) / References: UniProt: P00784, papain #2: Protein | Mass: 10197.745 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 2-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colocasia esculenta (taro) / Gene: CPI / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli BL21 (DE3) / References: UniProt: Q8L5J8 #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: 2.21 Å3/Da / Density % sol: 44.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG MME 2000, 0.1M Sodium Acetate trihydrate pH 4.6, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97315 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 39400 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.03→2.1 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3476 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PPN Resolution: 2.03→28.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 98515.52 / 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: 55.1294 Å2 / ksol: 0.36207 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→28.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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