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Yorodumi- PDB-1ye8: Crystal Structure of THEP1 from the hyperthermophile Aquifex aeolicus -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ye8 | ||||||
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Title | Crystal Structure of THEP1 from the hyperthermophile Aquifex aeolicus | ||||||
Components | Hypothetical UPF0334 kinase-like protein AQ_1292 | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / MIXED ALPHA-BETA PROTEIN / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / ATP binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Rossbach, M. / Daumke, O. / Klinger, C. / Wittinghofer, A. / Kaufmann, M. | ||||||
Citation | Journal: BMC Struct.Biol. / Year: 2005 Title: Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold Authors: Rossbach, M. / Daumke, O. / Klinger, C. / Wittinghofer, A. / Kaufmann, M. #1: Journal: BMC Biochem. / Year: 2003 Title: Thermophile-specific proteins: the gene product of aq_1292 from Aquifex aeolicus is an NTPase Authors: Klinger, C. / Rossbach, M. / Howe, R. / Kaufmann, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ye8.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ye8.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ye8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1ye8 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1ye8 | 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: 20734.068 Da / Num. of mol.: 1 / Mutation: M1MSE, M111MSE, M126MSE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1292 / Plasmid: PET101-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: O67322 | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: 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: 2.17 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG 3350, potassium dihydrogenphosphate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97625, 0.979802 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2003 / Details: Mirrors | |||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→18.21 Å / Num. all: 33181 / Num. obs: 33181 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.057 / Net I/σ(I): 11.67 | |||||||||
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.49 / Num. unique all: 11436 / Rsym value: 0.373 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→18.21 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.927 / SU ML: 0.038 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.304 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→18.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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