+Open data
-Basic information
Entry | Database: PDB / ID: 3wz5 | ||||||
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Title | Structure of the periplasmic domain of DotI (crystal form II) | ||||||
Components | DotI | ||||||
Keywords | UNKNOWN FUNCTION / type IVB secretion | ||||||
Function / homology | Type-IV b secretion system, inner-membrane complex component / Type-IV b secretion system, inner-membrane complex component / membrane / DotI Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Kuroda, T. / Kubori, T. / Uchida, Y. / Nagai, H. / Imada, K. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion Authors: Kuroda, T. / Kubori, T. / Thanh Bui, X. / Hyakutake, A. / Uchida, Y. / Imada, K. / Nagai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wz5.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wz5.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/3wz5 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/3wz5 | HTTPS FTP |
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-Related structure data
Related structure data | 3wz3C 3wz4SC C: citing same article (ref.) 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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3 |
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4 |
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Unit cell |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 15725.213 Da / Num. of mol.: 4 / Fragment: periplasmic domain, UNP residues 73-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: dotI, icmL / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O54626 |
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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: 4.05 Å3/Da / Density % sol: 69.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 0.2M NaCl, 40% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 35 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97923 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 1, 2010 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→81.4 Å / Num. all: 13479 / Num. obs: 13479 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 10.4 / Num. unique all: 1913 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WZ4 Resolution: 3.5→72.836 Å / SU ML: 0.63 / σ(F): 1.5 / Phase error: 18.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.86 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.5→72.836 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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