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Yorodumi- PDB-1dkg: CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dkg | ||||||
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Title | CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK | ||||||
Components |
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Keywords | COMPLEX (HSP24/HSP70) / HSP70 / GRPE / MOLECULAR CHAPERONE / NUCLEOTIDE EXCHANGE FACTOR / COILED-COIL / COMPLEX (HSP24-HSP70) / COMPLEX (HSP24-HSP70) complex | ||||||
Function / homology | Function and homology information protein-containing complex disassembly / stress response to copper ion / adenyl-nucleotide exchange factor activity / 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 ...protein-containing complex disassembly / stress response to copper ion / adenyl-nucleotide exchange factor activity / 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 / protein-folding chaperone binding / protein refolding / response to heat / DNA replication / protein-containing complex assembly / protein domain specific binding / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Harrison, C.J. / Kuriyan, J. | ||||||
Citation | Journal: Science / Year: 1997 Title: Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK. Authors: Harrison, C.J. / Hayer-Hartl, M. / Di Liberto, M. / Hartl, F. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dkg.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dkg.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dkg_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 1dkg_full_validation.pdf.gz | 500.3 KB | Display | |
Data in XML | 1dkg_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 1dkg_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/1dkg ftp://data.pdbj.org/pub/pdb/validation_reports/dk/1dkg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21882.854 Da / Num. of mol.: 2 / Mutation: CHAIN A, B, G122D Source method: isolated from a genetically manipulated source Details: ELASTASE PROTEOLYSIS PRODUCT, RESIDUES 34 - 197 / Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 (DE3) / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P09372 #2: Protein | | Mass: 41572.105 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN RESIDUES 3 - 383 / Mutation: CHAIN D, P319L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 (DE3) / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P04475, UniProt: P0A6Y8*PLUS #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: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Detector: CCD / Date: Oct 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 26024 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 29 % / Rsym value: 0.093 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.179 / % possible all: 86.4 |
Reflection | *PLUS Num. measured all: 754420 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 86.4 % / Rmerge(I) obs: 0.179 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION, TORSION ANGLE REFINEMENT
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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