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Yorodumi- PDB-4hyb: Crystal structure of the substrate binding domain of E.coli DnaK ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hyb | ||||||
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Title | Crystal structure of the substrate binding domain of E.coli DnaK in complex with pyrrhocoricin_LYZI (residues 1 to 10) | ||||||
Components |
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Keywords | CHAPERONE / PEPTIDE BINDING PROTEIN / antimicrobial peptide | ||||||
Function / homology | Function and homology information stress response to copper ion / sigma factor antagonist activity / chaperone cofactor-dependent protein refolding / protein unfolding / cellular response to unfolded protein / inclusion body / protein folding chaperone / 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 / inclusion body / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / ADP binding / unfolded protein binding / protein-folding chaperone binding / protein refolding / response to heat / DNA replication / protein-containing complex assembly / defense response to bacterium / innate immune response / ATP hydrolysis activity / protein-containing complex / zinc ion binding / extracellular region / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Pyrrhocoris apterus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.7 Å | ||||||
Authors | Zahn, M. / Straeter, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hyb.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hyb.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hyb_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 4hyb_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 4hyb_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4hyb_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/4hyb ftp://data.pdbj.org/pub/pdb/validation_reports/hy/4hyb | HTTPS FTP |
-Related structure data
Related structure data | 4eznC 4ezoC 4ezpC 4ezqC 4ezrC 4eztC 4ezwC 4ezxC 4ezyC 4ezzC 4f00C 4f01C 4hy9C 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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2 |
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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.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8 #2: Protein/peptide | Mass: 1352.663 Da / Num. of mol.: 2 / Fragment: UNP residues 1-10 / Source method: obtained synthetically Details: Pyrrhocoricin sequence occurs naturally in Pyrrhocoris apterus. Source: (synth.) Pyrrhocoris apterus (insect) / References: UniProt: P37362 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.37 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.6 Å / Num. obs: 60893 / % possible obs: 95.6 % |
Reflection shell | Resolution: 1.7→1.79 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: PDB ENTRY 3DPO / Resolution: 1.7→24.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.09 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / 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: 27.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 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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