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Yorodumi- PDB-1u14: The crystal structure of hypothetical UPF0244 protein yjjX at res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u14 | ||||||
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Title | The crystal structure of hypothetical UPF0244 protein yjjX at resolution 1.68 Angstrom | ||||||
Components | Hypothetical UPF0244 protein yjjX | ||||||
Keywords | STRUCTURAL GENOMICS / protein structure initiative / PSI / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information inosine/xanthosine triphosphatase / thiamine metabolic process / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.68 Å | ||||||
Authors | Qiu, Y. / Kim, Y. / Cuff, M. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of hypothetical UPF0244 protein yjjX at resolution 1.68 Angstrom Authors: Qiu, Y. / Kim, Y. / Cuff, M. / Collart, F. / Joachimiak, A. / Kossiakoff, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u14.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u14.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 1u14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/1u14 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/1u14 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18702.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: yjjX / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P39432 |
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#2: Chemical | ChemComp-PO4 / |
#3: 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: 2.55 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 150 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98020, 0.98036 | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 1, 2004 / Details: mirrors | |||||||||
Radiation | Monochromator: SI, 111, channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.68→50 Å / Num. obs: 37441 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 | |||||||||
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.445 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.68→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.861 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.104 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.397 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.723 Å / Total num. of bins used: 20 /
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