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Yorodumi- PDB-5btw: Structure of the N-terminal domain of lpg1496 from Legionella pne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5btw | ||||||
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Title | Structure of the N-terminal domain of lpg1496 from Legionella pneumophila | ||||||
Components | Uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / bacterial effector / alpha-beta fold / nucleotide-binding / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | SidE, PDE domain / SidE phosphodiesterase (PDE) domain / SidE PDE domain-containing protein Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Wong, K. / Kozlov, G. / 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 | 5btw.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5btw.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 5btw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/5btw ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5btw | HTTPS FTP |
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-Related structure data
Related structure data | 5btxC 5btySC 5btzC 5bu0C 5bu1C 5bu2C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16340.897 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-138) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1496 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZVE4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density % sol: 27.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate, 20% (w/v) PEG3350 |
-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: Mar 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 65120 / Num. obs: 60366 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.056 / Net I/σ(I): 43.9 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 6 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.8 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5BTY Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.279 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.044 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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