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Yorodumi- PDB-7n6j: Crystal structure of the substrate-binding domain of E. coli DnaK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n6j | ||||||||||||
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Title | Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RKQSTIALALLPLLFTPRR | ||||||||||||
Components |
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Keywords | CHAPERONE/HYDROLASE / Complex / Molecular chaperone / Protein/Peptide / CHAPERONE / CHAPERONE-HYDROLASE complex | ||||||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on phosphorus or arsenic in donors / stress response to copper ion / sigma factor antagonist activity / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / chaperone cofactor-dependent protein refolding / phosphoprotein phosphatase activity / protein unfolding / cellular response to unfolded protein ...oxidoreductase activity, acting on phosphorus or arsenic in donors / stress response to copper ion / sigma factor antagonist activity / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / chaperone cofactor-dependent protein refolding / phosphoprotein phosphatase activity / protein unfolding / cellular response to unfolded protein / dephosphorylation / inclusion body / protein folding chaperone / heat shock protein binding / protein dephosphorylation / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / outer membrane-bounded periplasmic space / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / periplasmic space / magnesium ion binding / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Jansen, R.M. / Ozden, C. / Gierasch, L.M. / Garman, S.C. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein. Authors: Clerico, E.M. / Pozhidaeva, A.K. / Jansen, R.M. / Ozden, C. / Tilitsky, J.M. / Gierasch, L.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n6j.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n6j.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 7n6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n6j ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n6j | HTTPS FTP |
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-Related structure data
Related structure data | 7jmmC 7jn8C 7jn9C 7jneC 7n6kC 7n6lC 7n6mC 1dkzS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23820.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8 | ||||
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#2: Protein/peptide | Mass: 2198.696 Da / Num. of mol.: 1 / Mutation: M1R, V18R, T19R / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P00634, alkaline phosphatase | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M (NH4)2SO4, 0.1 M K3PO4 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K throughout the collection / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: May 1, 2019 / Details: Rigaku VariMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 17179 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.068 / Rrim(I) all: 0.167 / Χ2: 1.768 / Net I/σ(I): 5.2 / Num. measured all: 107879 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DKZ Resolution: 2→33.93 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.938 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 91.35 Å2 / Biso mean: 31.462 Å2 / Biso min: 16.95 Å2
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Refinement step | Cycle: final / Resolution: 2→33.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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