+Open data
-Basic information
Entry | Database: PDB / ID: 5obx | ||||||
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Title | Mycoplasma genitalium DnaK-NBD | ||||||
Components | Chaperone protein DnaK | ||||||
Keywords | CHAPERONE / Complex / co-factor / ATP hydrolysis | ||||||
Function / homology | Function and homology information chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycoplasma genitalium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Adell, M. / Calisto, B. / Fita, I. / Martinelli, L. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Protein Sci. / Year: 2018 Title: The nucleotide-bound/substrate-bound conformation of the Mycoplasma genitalium DnaK chaperone. Authors: Adell, M. / Calisto, B.M. / Fita, I. / Martinelli, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5obx.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5obx.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 5obx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5obx_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 5obx_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 5obx_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 5obx_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/5obx ftp://data.pdbj.org/pub/pdb/validation_reports/ob/5obx | HTTPS FTP |
-Related structure data
Related structure data | 5obuC 5obvC 5obwSC 5obyC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40749.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Contains a C-terminal hexa-histidine tag. / Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: dnaK, hsp70, MG305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47547 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PGE / | #4: Chemical | #5: 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: 3.86 Å3/Da / Density % sol: 68.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, ammonium sulfate, potassium thiocyanate / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2014 |
Radiation | Monochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→78.96 Å / Num. obs: 57432 / % possible obs: 99.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.02 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8302 / Rpim(I) all: 0.36 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OBW Resolution: 1.78→45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.756 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.161 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→45 Å
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Refine LS restraints |
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