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- PDB-4jwi: 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: 4jwi | ||||||
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Title | Crystal structure of the substrate binding domain of E.coli DnaK in complex with sheep Bac7(35-43) | ||||||
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![]() | CHAPERONE/ANTIBIOTIC / chaperone / peptide binding / antimicrobial peptide / CHAPERONE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / DNA replication / defense response to bacterium / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zahn, M. / Straeter, N. | ||||||
![]() | ![]() Title: Structural Identification of DnaK Binding Sites within Bovine and Sheep Bactenecin Bac7. Authors: Zahn, M. / Kieslich, B. / Berthold, N. / Knappe, D. / Hoffmann, R. / Strater, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.4 KB | Display | ![]() |
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PDB format | ![]() | 149.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.4 KB | Display | ![]() |
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Full document | ![]() | 463.5 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jwcC ![]() 4jwdC ![]() 4jweC ![]() 3dpoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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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.: 2 / Fragment: unp residues 389-607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1147.438 Da / Num. of mol.: 2 / Fragment: unp residues 165-173 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 2.2 M ammonium sulfate, 0.1 M citric acid, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→23.79 Å / Num. obs: 45783 / % possible obs: 99.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.414 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3DPO Resolution: 1.9→23.79 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9106 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.259 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→23.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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