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- PDB-7jmm: Crystal structure of the substrate-binding domain of E. coli DnaK... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jmm | |||||||||
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Title | Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RAKNIILLSR | |||||||||
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![]() | CHAPERONE / Complex / Molecular chaperone / Protein/Peptide | |||||||||
Function / homology | ![]() 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 / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / 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 / phosphoprotein phosphatase activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / dephosphorylation / protein folding chaperone / inclusion body / heat shock protein binding / protein dephosphorylation / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / outer membrane-bounded periplasmic space / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Jansen, R.M. / Ozden, C. / Gierasch, L.M. / Garman, S.C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
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PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jn8C ![]() 7jn9C ![]() 7jneC ![]() 7n6jC ![]() 7n6kC ![]() 7n6lC ![]() 7n6mC ![]() 1dkzS C: citing same article ( S: Starting model for refinement |
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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: 23820.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 1186.472 Da / Num. of mol.: 1 / Mutation: P63R, I71S, G72R / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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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 |
-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: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jun 27, 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: 2.56→50 Å / Num. obs: 7236 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.079 / Rrim(I) all: 0.161 / Χ2: 2.211 / Net I/σ(I): 5.2 / Num. measured all: 43951 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DKZ Resolution: 2.56→47.79 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.845 / SU B: 19.94 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.108 / ESU R Free: 0.411 / 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: 92.24 Å2 / Biso mean: 46.278 Å2 / Biso min: 30.17 Å2
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Refinement step | Cycle: final / Resolution: 2.56→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.622 Å / Rfactor Rfree error: 0
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