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Yorodumi- PDB-5bty: Structure of the middle domain of lpg1496 from Legionella pneumop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bty | ||||||
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Title | Structure of the middle domain of lpg1496 from Legionella pneumophila in P21 space group | ||||||
Components | lpg1496 | ||||||
Keywords | UNKNOWN FUNCTION / bacterial effector / alpha-beta fold / nucleotide binding / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å | ||||||
Authors | Kozlov, G. / Zhang, Y. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structure of the Legionella Effector, lpg1496, Suggests a Role in Nucleotide Metabolism. Authors: Wong, K. / Kozlov, G. / Zhang, Y. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bty.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bty.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/5bty ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5bty | HTTPS FTP |
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-Related structure data
Related structure data | 5btwC 5btxC 5btzC 5bu0C 5bu1C 5bu2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15399.021 Da / Num. of mol.: 1 / Fragment: UNP residues 152-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria) Gene: lp12_1434 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G8UY02 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 42458 / Num. obs: 39061 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.068 / Net I/σ(I): 43.2 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / % possible all: 57.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→40.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.059 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 13.281 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→40.47 Å
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Refine LS restraints |
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