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Yorodumi- PDB-5oow: Crystal structure of lobe II from the nucleotide binding domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oow | ||||||
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Title | Crystal structure of lobe II from the nucleotide binding domain of DnaK in complex with AMPPCP | ||||||
Components | Chaperone protein DnaK | ||||||
Keywords | CHAPERONE / Hsp70 / nucleotide binding domain / NBD / sugar kinase family | ||||||
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 / ADP 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 / ADP binding / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / protein-containing complex assembly / DNA replication / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Jakob, R.P. / Bauer, D. / Meinhold, S. / Stigler, J. / Merkel, U. / Maier, T. / Rief, M. / Zoldak, G. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy. Authors: Bauer, D. / Meinhold, S. / Jakob, R.P. / Stigler, J. / Merkel, U. / Maier, T. / Rief, M. / Zoldak, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oow.cif.gz | 299.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oow.ent.gz | 247.1 KB | Display | PDB format |
PDBx/mmJSON format | 5oow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/5oow ftp://data.pdbj.org/pub/pdb/validation_reports/oo/5oow | HTTPS FTP |
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-Related structure data
Related structure data | 4jn4S S: Starting model for refinement |
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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
#1: Protein | Mass: 22458.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: dnaK, groP, grpF, seg, b0014, JW0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6Y8 #2: Chemical | #3: 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: 2.93 Å3/Da / Density % sol: 58.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG1500, 0.1 M MIB buffer pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→54.74 Å / Num. obs: 11517 / % possible obs: 98.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 69.16 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.157 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.966 / Num. unique obs: 1846 / CC1/2: 0.73 / Rpim(I) all: 0.597 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JN4 Resolution: 2.9→54.74 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.374
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Displacement parameters | Biso mean: 57.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→54.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.18 Å / Total num. of bins used: 6
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Refinement TLS params. | T22: -0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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