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Yorodumi- PDB-1yx1: Crystal Structure of Protein of Unknown Function PA2260 from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yx1 | ||||||
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Title | Crystal Structure of Protein of Unknown Function PA2260 from Pseudomonas aeruginosa, Possible Sugar Phosphate Isomerase | ||||||
Components | hypothetical protein PA2260 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PA2260 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ISOPROPYL ALCOHOL / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Osipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of hypothetical protein PA2260 from Pseudomonas aeruginosa Authors: Osipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yx1.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yx1.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yx1_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 1yx1_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 1yx1_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 1yx1_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yx1 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yx1 | HTTPS FTP |
-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: 29494.018 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA2260 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I1L3 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: 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: 2.7 Å3/Da / Density % sol: 53.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis_Tris pH 6.5, 8% PEG 5000 MME, 4% isopropyl alcohol, 50 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 / Wavelength: 0.97943 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 26, 2004 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 80010 / Num. obs: 75770 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.32 / % possible all: 59.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 3.281 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 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 mean: 27.331 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.795→1.842 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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