+Open data
-Basic information
Entry | Database: PDB / ID: 5ot4 | ||||||
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Title | Structure of the Legionella pneumophila effector RidL (1-866) | ||||||
Components | Interaptin | ||||||
Keywords | TRANSPORT PROTEIN / Retromer / Legionella pneumophila | ||||||
Function / homology | : / Interaptin Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Romano-Moreno, M. / Rojas, A.L. / Lucas, M. / Isupov, M.N. / Hierro, A. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL. Authors: Romano-Moreno, M. / Rojas, A.L. / Williamson, C.D. / Gershlick, D.C. / Lucas, M. / Isupov, M.N. / Bonifacino, J.S. / Machner, M.P. / Hierro, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ot4.cif.gz | 641 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ot4.ent.gz | 536.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ot4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5ot4 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5ot4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 101506.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lp12_2303 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UZ99, UniProt: Q5ZT54*PLUS #2: Chemical | ChemComp-GOL / | |
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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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.4 M sodium fluoride, 14-16% PEG 3350 0.1 M Bis-tris propane pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→167.27 Å / Num. obs: 93761 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.954 % / Biso Wilson estimate: 104.762 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.012 / Net I/σ(I): 12.6 / Num. measured all: 651993 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3→167.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 32.879 / SU ML: 0.536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 220 Å2 / Biso mean: 122.624 Å2 / Biso min: 58.45 Å2
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Refinement step | Cycle: final / Resolution: 3→167.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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