+Open data
-Basic information
Entry | Database: PDB / ID: 4kun | ||||||
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Title | Crystal structure of Legionella pneumophila Lpp1115 / KaiB | ||||||
Components | Hypothetical protein Lpp1115Hypothesis | ||||||
Keywords | UNKNOWN FUNCTION / Midwest Center for Structural Genomics / MCSG / PSI-Biology / Alpha and beta proteins (a/b) / thioredoxin fold | ||||||
Function / homology | Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Petit, P. / Stogios, P.J. / Stein, A. / Wawrzak, Z. / Skarina, T. / Daniels, C. / Di Leo, R. / Buchrieser, C. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Environ Microbiol / Year: 2014 Title: The Legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments. Authors: Loza-Correa, M. / Sahr, T. / Rolando, M. / Daniels, C. / Petit, P. / Skarina, T. / Gomez Valero, L. / Dervins-Ravault, D. / Honore, N. / Savchenko, A. / Buchrieser, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kun.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kun.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kun ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kun | 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: 10168.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lpp1115 / Plasmid: p15Tv-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q5X655 #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: 2.01 Å3/Da / Density % sol: 38.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium acetate, 0.1 M bis-Tris pH 6.5, 35% w/v PEG 8K, 1 mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2828144 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2828144 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.91 Å / Num. obs: 11748 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1686 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→27.379 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→27.379 Å
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Refine LS restraints |
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LS refinement shell |
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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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