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Yorodumi- PDB-4rtf: Crystal structure of molecular chaperone DnaK from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rtf | ||||||
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Title | Crystal structure of molecular chaperone DnaK from Mycobacterium tuberculosis H37Rv | ||||||
Components | Chaperone protein DnaK | ||||||
Keywords | CHAPERONE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / DnaK | ||||||
Function / homology | ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta / ADENOSINE-5'-TRIPHOSPHATE / : Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Endres, M. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of molecular chaperone DnaK from Mycobacterium tuberculosis H37Rv Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Endres, M. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rtf.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rtf.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 4rtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rtf_validation.pdf.gz | 799.9 KB | Display | wwPDB validaton report |
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Full document | 4rtf_full_validation.pdf.gz | 807.8 KB | Display | |
Data in XML | 4rtf_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 4rtf_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/4rtf ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rtf | HTTPS FTP |
-Related structure data
Related structure data | 2v7yS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 59481.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: dnaK, P425_00363, RVBD_0350, WP_003401814 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: I6Y7L1 |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-PG4 / |
#4: 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: 2.27 Å3/Da / Density % sol: 45.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Ammonium Chloride, 0.1 M HEPES, 20% PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2014 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→30 Å / Num. all: 14714 / Num. obs: 14714 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 52.8 |
Reflection shell | Resolution: 2.77→2.82 Å / Redundancy: 22 % / Rmerge(I) obs: 0.64 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V7Y Resolution: 2.77→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 27.694 / SU ML: 0.275 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.521 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 68.437 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→30 Å
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Refine LS restraints |
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