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Yorodumi- PDB-3llb: The crystal structure of the protein PA3983 with unknown function... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3llb | ||||||
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Title | The crystal structure of the protein PA3983 with unknown function from Pseudomonas aeruginosa PAO1 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown function / protein PA3983 / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhang, R. / Kagan, O. / Savchenko, A. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the protein NE1376 with unknown function from Nitrosomonas europaea ATCC 19718 Authors: Zhang, R. / Kagan, O. / Savchenko, A. / Joachimiak, 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 | 3llb.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3llb.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 3llb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3llb_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 3llb_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 3llb_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 3llb_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3llb ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3llb | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9368.580 Da / Num. of mol.: 1 / Fragment: Sequence database residues 197-279 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: GI:15599178, PA3983 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HX36 |
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#2: 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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, MgCl2 0.2M, Bis-Tris 0.1M, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→51.64 Å / Num. all: 7735 / Num. obs: 7457 / % possible obs: 96.45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 57.03 |
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.1 / Num. unique all: 566 / % possible all: 77.74 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→51.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.51 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.139 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 11.429 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→51.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.638 Å / Origin y: -3.422 Å / Origin z: 2.27 Å
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Refinement TLS group |
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