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Yorodumi- PDB-4ezo: Crystal structure of the substrate binding domain of E.coli DnaK ... -
+Open data
-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) | ||||||
Components |
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Keywords | CHAPERONE/PEPTIDE BINDING PROTEIN / chaperone / peptide binding / CHAPERONE-PEPTIDE BINDING PROTEIN complex | ||||||
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 / 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 / inclusion body / protein folding chaperone / 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 / protein refolding / response to heat / DNA replication / protein-containing complex assembly / defense response to Gram-negative bacterium / 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 | Escherichia coli (E. coli) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3DPO / Resolution: 1.9 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 | 4ezo.cif.gz | 184.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ezo.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ezo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ezo_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 4ezo_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 4ezo_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4ezo_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/4ezo ftp://data.pdbj.org/pub/pdb/validation_reports/ez/4ezo | 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 (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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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.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0014, dnaK, groP, grpF, JW0013, seg / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y8 #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.) Sus scrofa (pig) / References: UniProt: P80054 #3: Chemical | ChemComp-SO4 / #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: 2.72 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
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 |
-Processing
Software |
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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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