+Open data
-Basic information
Entry | Database: PDB / ID: 4zuz | ||||||
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Title | SidC 1-871 | ||||||
Components | SidC | ||||||
Keywords | Phosphate Binding Protein / SIDC / P4C / PI4P binding domain | ||||||
Function / homology | : / : / SidC, C-terminal domain / SidC, lipid-binding domain / SidC, N-terminal / SidC N-terminal domain / Protein SdcA Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Luo, X. / Wasilko, D.J. / Liu, Y. / Sun, J. / Wu, X. / Luo, Z.-Q. / Mao, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos Pathog. / Year: 2015 Title: Structure of the Legionella Virulence Factor, SidC Reveals a Unique PI(4)P-Specific Binding Domain Essential for Its Targeting to the Bacterial Phagosome. Authors: Luo, X. / Wasilko, D.J. / Liu, Y. / Sun, J. / Wu, X. / Luo, Z.Q. / Mao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zuz.cif.gz | 356.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zuz.ent.gz | 286.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zuz_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 4zuz_full_validation.pdf.gz | 517.9 KB | Display | |
Data in XML | 4zuz_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 4zuz_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/4zuz ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zuz | HTTPS FTP |
-Related structure data
Related structure data | 4irhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 105901.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6RCR4 #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: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, Hepes, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9759 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→50 Å / Num. obs: 53345 / % possible obs: 100 % / Redundancy: 5 % / Net I/σ(I): 46.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IRH Resolution: 2.86→49.16 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.895 / SU B: 39.05 / SU ML: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: 204.42 Å2 / Biso mean: 77.471 Å2 / Biso min: 25.43 Å2
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Refinement step | Cycle: final / Resolution: 2.86→49.16 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.861→2.935 Å / Total num. of bins used: 20
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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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