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Yorodumi- PDB-7n6m: Crystal structure of the substrate-binding domain of E. coli DnaK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n6m | ||||||||||||
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Title | Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RQKPLLGLSR | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 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 | 7n6m.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n6m.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 7n6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n6m ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n6m | HTTPS FTP |
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-Related structure data
Related structure data | 7jmmC 7jn8C 7jn9C 7jneC 7n6jC 7n6kC 7n6lC 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: 1170.429 Da / Num. of mol.: 1 / Mutation: Q273R, F281S, A282R / 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: 2.11 Å3/Da / Density % sol: 41.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.6 M (NH4)2SO4, 0.1 M K3PO4 |
-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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.82→74.04 Å / Num. obs: 18615 / % possible obs: 96.3 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.05 / Rrim(I) all: 0.163 / Net I/σ(I): 8.4 / Num. measured all: 186551 / Scaling rejects: 651 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 10.1 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DKZ Resolution: 1.82→74.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.804 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.167 / 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: 103.29 Å2 / Biso mean: 36.988 Å2 / Biso min: 21.33 Å2
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Refinement step | Cycle: final / Resolution: 1.82→74.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.822→1.869 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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