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Yorodumi- PDB-4l7m: Crystal structure of the archaeal HEAT-like repeats protein TON_1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l7m | |||||||||
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Title | Crystal structure of the archaeal HEAT-like repeats protein TON_1937 from Thermococcus onnurineus NA1 | |||||||||
Components | Putative uncharacterized protein | |||||||||
Keywords | UNKNOWN FUNCTION / HEAT-repeats / Hypothetical | |||||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Uncharacterized protein Function and homology information | |||||||||
Biological species | Thermococcus onnurineus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å | |||||||||
Authors | Kim, Y.G. / Jeong, J.H. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the archaeal HEAT-like repeats protein TON_1937 from Thermococcus onnurineus NA1 Authors: Kim, Y.G. / Jeong, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l7m.cif.gz | 207.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l7m.ent.gz | 175.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l7m ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l7m | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30418.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: Thermococcus Onnurineus, TON_1937 / Plasmid: pProExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: B6YW62 #2: Chemical | #3: 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: 2.37 Å3/Da / Density % sol: 48.05 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100mM Tris-HCl, pH 8.0, 0.8M ammonium acetate, 8% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2011 / Details: mirrors |
Radiation | Monochromator: a silicon double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 38857 / % possible obs: 93.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6.4 / Redundancy: 4.3 % / Biso Wilson estimate: 32.23 Å2 / Rsym value: 0.037 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.211 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.002→28.5 Å / SU ML: 0.25 / σ(F): 1.54 / Phase error: 24.92 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→28.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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Refinement TLS params. | Method: refined / Origin x: -23.9389 Å / Origin y: 8.9465 Å / Origin z: -0.205 Å
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Refinement TLS group | Selection details: ALL |