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- PDB-3wdc: N-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wdc | ||||||
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Title | N-terminal domain of Mycobacterium tuberculosis ClpC1 bound to Cyclomarin A | ||||||
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![]() | Chaperone/Antimicrobial protein / Chaperone / Chaperone-Antimicrobial protein complex | ||||||
Function / homology | ![]() protein folding chaperone / peptidoglycan-based cell wall / cellular response to heat / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vasudevan, D. / Noble, C.G. | ||||||
![]() | ![]() Title: Structural basis of mycobacterial inhibition by cyclomarin A Authors: Vasudevan, D. / Rao, S.P.S. / Noble, C.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.4 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wdbSC ![]() 3wddC ![]() 3wdeC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17073.557 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 0.2M ammonium acetate, 20% polyethylene glycol 3350, 0.025M magnesium, pH 7.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→45 Å / Num. obs: 42423 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WDB Resolution: 1.18→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.924 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 100.35 Å2 / Biso mean: 13.093 Å2 / Biso min: 3.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.18→1.211 Å / Total num. of bins used: 20
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