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- PDB-4ezu: 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: 4ezu | ||||||
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Title | Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-bombesin in space group I222 | ||||||
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![]() | CHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex | ||||||
Function / homology | ![]() stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / ATP-dependent protein folding chaperone ...stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / neuropeptide signaling pathway / 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 / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() Bombina maxima (large-webbed bell toad) | ||||||
Method | ![]() ![]() | ||||||
![]() | Zahn, M. / Straeter, N. | ||||||
![]() | ![]() Title: Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes Authors: Zahn, M. / Straeter, 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 | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 78 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23820.777 Da / Num. of mol.: 1 / Fragment: UNP residues 389-607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2040.453 Da / Num. of mol.: 1 / Fragment: UNP residues 46-60 / Source method: obtained synthetically Details: This sequence occurs naturally in Bombina maxima. C-terminus is amidated. Source: (synth.) Bombina maxima (large-webbed bell toad) / References: UniProt: Q8QFP2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.0 M ammonium sulfate, 0.1 M HEPES pH 8.0, 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: Oct 19, 2010 |
Radiation | Monochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 17741 / % possible obs: 99.8 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.558 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: PDB ID 1DKZ / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.73 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 35.847 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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