+Open data
-Basic information
Entry | Database: PDB / ID: 3zpj | ||||||
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Title | Crystal structure of Ton1535 from Thermococcus onnurineus NA1 | ||||||
Components | TON_1535 | ||||||
Keywords | UNKNOWN FUNCTION / SOLENOID PROTEIN / HYPOTHETICAL PROTEIN / RIGHT-HANDED COILED COIL / LEFT-HANDED HELIX TURN | ||||||
Function / homology | Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / Uncharacterized protein Function and homology information | ||||||
Biological species | THERMOCOCCUS ONNURINEUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.304 Å | ||||||
Authors | Jeong, J.H. / kim, Y.G. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Structure of the Hypothetical Protein Ton1535 from Thermococcus Onnurineus Na1 Reveals Unique Structural Properties by a Left-Handed Helical Turn in Normal Alpha-Solenoid Protein. Authors: Jeong, J. / Kim, Y. / Rojvirija, C. / Cha, H.J. / Kim, Y. / Ha, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zpj.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zpj.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/3zpj ftp://data.pdbj.org/pub/pdb/validation_reports/zp/3zpj | 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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Unit cell |
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-Components
#1: Protein | Mass: 40954.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS ONNURINEUS (archaea) / Strain: NA1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) RIL / References: UniProt: B6YTT4 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M BIS-TRIS PROPANE (PH7.0), 1.2 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 24870 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 41.33 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 45.5 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9.7 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.304→29.911 Å / SU ML: 0.29 / σ(F): 1.29 / Phase error: 24.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.304→29.911 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 13.2702 Å / Origin y: 12.7587 Å / Origin z: 41.1984 Å
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Refinement TLS group | Selection details: ALL |