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Yorodumi- PDB-1yll: Crystal Structure of the Conserved Protein of Unknown Function PA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yll | ||||||
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Title | Crystal Structure of the Conserved Protein of Unknown Function PA5104 from Pseudomonas aeruginosa PAO1 | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / beta-barrels / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Uncharacterised protein family HutD/Ves / HutD / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 Å | ||||||
Authors | Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Conserved Hypothetical Protein PA5104 from Pseudomonas aeruginosa PAO1 Authors: Kim, Y. / Joachimiak, A. / Skarina, T. / Savchenko, A. / Edwards, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yll.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yll.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yll_validation.pdf.gz | 461.1 KB | Display | wwPDB validaton report |
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Full document | 1yll_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 1yll_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 1yll_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/1yll ftp://data.pdbj.org/pub/pdb/validation_reports/yl/1yll | 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: 21873.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9HU79 #2: 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 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, magnesium chloride, Tris, L-lysine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9794, 0.956 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.64→77.15 Å / Num. all: 84910 / Num. obs: 82845 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.4 | ||||||||||||
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.7 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.64→77.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / 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: 24.223 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→77.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.641→1.683 Å / Total num. of bins used: 20 /
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