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Yorodumi- PDB-3l18: Ton1285, an Intracellular Protease from Thermococcus onnurineus NA1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l18 | ||||||
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Title | Ton1285, an Intracellular Protease from Thermococcus onnurineus NA1 | ||||||
Components | Intracellular protease I | ||||||
Keywords | HYDROLASE / GATase1_PfpI_like / Protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermococcus onnurineus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Jung, H.J. / Cha, S.S. | ||||||
Citation | Journal: To be Published Title: Structure Based Classification of the DJ-1 Superfamily: The Relationship between Homologous Structures and Various Functions Authors: Jung, H.J. / Cha, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l18.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l18.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 3l18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/3l18 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/3l18 | HTTPS FTP |
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-Related structure data
Related structure data | 1g2iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 165 / Label seq-ID: 4 - 167
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-Components
#1: Protein | Mass: 18888.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: intracellular protease I / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B6YXG0 #2: 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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 8 Details: 20% PEG 8000, 0.1M HEPES pH7.5, 0.2M Ammonium sulfate, pH 8.0, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 31234 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.78→50 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 4.23 / Num. unique all: 32912 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G2I Resolution: 1.78→29.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.155 / SU ML: 0.074 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.9 Å2 / Biso mean: 19.725 Å2 / Biso min: 12.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→29.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1300 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.784→1.83 Å / Total num. of bins used: 20
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