+Open data
-Basic information
Entry | Database: PDB / ID: 2ych | ||||||
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Title | PilM-PilN type IV pilus biogenesis complex | ||||||
Components |
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Keywords | CELL CYCLE / TYPE IV PILUS ACTIN SECRETION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Karuppiah, V. / Derrick, J.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure of the Pilm-Piln Inner Membrane Type Iv Pilus Biogenesis Complex from Thermus Thermophilus. Authors: Karuppiah, V. / Derrick, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ych.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ych.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ych.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2ych ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2ych | HTTPS FTP |
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-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: 41700.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843(DE3) / References: UniProt: Q5SIJ0, UniProt: Q72IW8*PLUS |
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#2: Protein/peptide | Mass: 1897.406 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-15 / Source method: obtained synthetically / Source: (synth.) THERMUS THERMOPHILUS (bacteria) / References: UniProt: Q5SII9, UniProt: Q72IW7*PLUS |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
Sequence details | F334L DUE TO PCR ERROR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 0.55 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M TRIS PH 8.0, 0.2M MAGNESIUM CHLORIDE AND 20% (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→91 Å / Num. obs: 27534 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 13.3 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.16→2.21 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.2→50.3 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.55 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.209 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OMITTED RESIDUES ARE 1-10 AT THE N-TERMINUS, 250-274. BETWEEN ALPHA7 AND ALPHA8, AND 376-377 AT THE C-TERMINUS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.861 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50.3 Å
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Refine LS restraints |
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