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Yorodumi- PDB-1kid: GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kid | ||||||
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Title | GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES 191-376, MUTANT WITH ALA 262 REPLACED WITH LEU AND ILE 267 REPLACED WITH MET | ||||||
Components | GROEL (HSP60 CLASS) | ||||||
Keywords | CHAPERONE / HSP60 / GROEL / CELL DIVISION / ATP-BINDING / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Buckle, A.M. / Fersht, A.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: A structural model for GroEL-polypeptide recognition. Authors: Buckle, A.M. / Zahn, R. / Fersht, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kid.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kid.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kid_validation.pdf.gz | 360.4 KB | Display | wwPDB validaton report |
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Full document | 1kid_full_validation.pdf.gz | 362.6 KB | Display | |
Data in XML | 1kid_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1kid_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1kid ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1kid | HTTPS FTP |
-Related structure data
Related structure data | 1jonS 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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Unit cell |
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Details | RESIDUES 184 - 190 (PART OF A FUSED N-TERMINAL TAG) BINDS IN THE PUTATIVE POLYPEPTIDE-BINDING SITE OF A NEIGHBORING MOLECULE IN THE CRYSTAL LATTICE. THIS "MINI-CHAPERONE - PEPTIDE COMPLEX" CAN BE GENERATED BY APPLYING THE TRANSFORMATION 1/2 - X, -Y, 1/2+Z TO THE N-TERMINAL TAG (RESIDUES 184 - 190) AND COMBINING THE RESULTING COORDINATES WITH RESIDUES. |
-Components
#1: Protein | Mass: 22060.316 Da / Num. of mol.: 1 / Fragment: APICAL DOMAIN, RESIDUES 191 - 376 / Mutation: A262L, I267M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Cellular location: CYTOPLASM / Plasmid: PRSET (INVITROGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.07 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→12.8 Å / Num. obs: 25290 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2 / % possible all: 85.6 |
Reflection | *PLUS Num. measured all: 260633 |
Reflection shell | *PLUS % possible obs: 85.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RESIDUES 191 - 345 OF PDB ENTRY 1JON Resolution: 1.7→12.8 Å / σ(F): 0
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Displacement parameters | Biso mean: 17.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→12.8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |