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- PDB-5bu1: Structure of the truncated C-terminal domain of lpg1496 from Legi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bu1 | ||||||
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Title | Structure of the truncated C-terminal domain of lpg1496 from Legionella pneumophila | ||||||
![]() | LPG1496 | ||||||
![]() | UNKNOWN FUNCTION / bacterial effector / nucleotide-binding / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | MALONATE ION / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wong, K. / Kozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 59.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.2 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5btwC ![]() 5btxC ![]() 5btyC ![]() 5btzC ![]() 5bu0SC ![]() 5bu2C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33757.078 Da / Num. of mol.: 1 / Fragment: UNP residues 293-580 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lp12_1434 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MLI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1 M sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 42638 / Num. obs: 42595 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rsym value: 0.093 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 8.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BU0 Resolution: 1.6→29.61 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.337 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.084 / 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: 18.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.61 Å
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Refine LS restraints |
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