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- PDB-4ezo: 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: 4ezo | ||||||
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Title | Crystal structure of the substrate binding domain of E.coli DnaK in complex with PR-39 (residues 1 to 15) | ||||||
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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 / cellular response to unfolded protein / protein folding chaperone / inclusion body / heat shock protein binding / lipopolysaccharide binding / ATP-dependent protein folding chaperone ...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 / lipopolysaccharide binding / ATP-dependent protein folding chaperone / ADP binding / antimicrobial humoral immune response mediated by antimicrobial peptide / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / protein-containing complex assembly / defense response to Gram-negative bacterium / DNA replication / defense response to Gram-positive bacterium / innate immune response / ATP hydrolysis activity / protein-containing complex / extracellular space / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zahn, M. / Straeter, N. | ||||||
![]() | ![]() Title: Structural Studies on the Forward and Reverse Binding Modes of Peptides to the Chaperone DnaK. Authors: Zahn, M. / Berthold, N. / Kieslich, B. / Knappe, D. / Hoffmann, R. / Strater, N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.3 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.5 KB | Display | ![]() |
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Full document | ![]() | 468 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4eznC ![]() 4ezpC ![]() 4ezqC ![]() 4ezrC ![]() 4eztC ![]() 4ezwC ![]() 4ezxC ![]() 4ezyC ![]() 4ezzC ![]() 4f00C ![]() 4f01C ![]() 4hy9C ![]() 4hybC 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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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.: 2 / Fragment: UNP residues 389-607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1917.313 Da / Num. of mol.: 2 / Fragment: UNP residues 131-145 / Source method: obtained synthetically / Details: This sequence occurs naturally in pigs. / 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: 2.72 Å3/Da / Density % sol: 54.74 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 2.4 M ammonium sulfate, 0.1 M citric acid pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011 |
Radiation | Monochromator: Si - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→24.8 Å / Num. obs: 45171 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.457 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: PDB ENTRY 3DPO / Resolution: 1.9→24.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.407 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / 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: 41.101 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.8 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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