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Yorodumi- PDB-4mu6: Crystal Structure of the N-terminal domain of Effector Protein Le... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mu6 | ||||||
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Title | Crystal Structure of the N-terminal domain of Effector Protein LegC3 from Legionella pneumophila | ||||||
Components | Kinectin 1 (Kinesin receptor) | ||||||
Keywords | UNKNOWN FUNCTION / structural genomics | ||||||
Function / homology | LegC3 N-terminal, Legionellaceae / LegC3 N-terminal coiled-coil domain / membrane => GO:0016020 / Kinectin 1 (Kinesin receptor) Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.082 Å | ||||||
Authors | Yao, D. / Cherney, M. / Cygler, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the N-terminal domain of the effector protein LegC3 from Legionella pneumophila. Authors: Yao, D. / Cherney, M. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mu6.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mu6.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mu6_validation.pdf.gz | 421 KB | Display | wwPDB validaton report |
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Full document | 4mu6_full_validation.pdf.gz | 422.2 KB | Display | |
Data in XML | 4mu6_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4mu6_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/4mu6 ftp://data.pdbj.org/pub/pdb/validation_reports/mu/4mu6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42789.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: legC3, lpg1701 / Plasmid: pZL922 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q5ZUU1 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG3300, 0.1MTris-HCl pH8.5, 0.2M tri-potassium citrate, 30mM Di-ammonium hydrogen phosphate, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97887 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97887 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→50 Å / Num. obs: 23598 / % possible obs: 94.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 7.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.082→45.499 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 29.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.082→45.499 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.9159 Å / Origin y: 36.0438 Å / Origin z: 13.7062 Å
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Refinement TLS group | Selection details: all |