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Yorodumi- PDB-1kp8: Structural Basis for GroEL-assisted Protein Folding from the Crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kp8 | |||||||||
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Title | Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution | |||||||||
Components | groEL protein | |||||||||
Keywords | CHAPERONE / chaperonin / GroEL / assisted protein folding | |||||||||
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 / Resolution: 2 Å | |||||||||
Authors | Wang, J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution Authors: Wang, J. / Boisvert, D.C. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: The 2.4 A Crystal Structure of the Bacterial Chaperonin GroEL Complexed with ATP Gamma S Authors: Boisvert, D.C. / Wang, J. / Otwinowski, Z. / Horwich, A.L. / Sigler, P.B. #2: Journal: Nature / Year: 1994 Title: The Crystal Structure of the Bacterial Chaperonin GroEL at 2.8 A Authors: Braig, K. / Otwinowski, Z. / Hegde, R. / Boisvert, D.C. / Joachimiak, A. / Horwich, A.L. / Sigler, P.B. #3: Journal: Nat.Struct.Biol. / Year: 1995 Title: Conformational Variability in the Refined Structure of the Chaperonin GroEL at 2.8 A Resolution Authors: Braig, K. / Adams, P.D. / Brunger, A.T. #4: Journal: Nature / Year: 1997 Title: The Crystal Structure of the Asymmetric GroEL-GroES-(ADP)7 Chaperonin Complex Authors: Xu, Z. / Horwich, A.L. / Sigler, P.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kp8.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1kp8.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1kp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kp8_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 1kp8_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 1kp8_validation.xml.gz | 298.9 KB | Display | |
Data in CIF | 1kp8_validation.cif.gz | 403.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/1kp8 ftp://data.pdbj.org/pub/pdb/validation_reports/kp/1kp8 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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-Components
-Protein , 1 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | Mass: 57130.379 Da / Num. of mol.: 14 / Mutation: R13G, A126V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5 |
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-Non-polymers , 5 types, 2607 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-AGS / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.13 % Description: The diffraction data used in remark 200 was extracted from PDB entry 1der. |
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Crystal grow | *PLUS Method: other / Details: Ranson, N.A., (1998) Biochem. J., 333, 233. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 646053 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.096 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 540791 / % possible obs: 99.1 % / Num. measured all: 645898 / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Resolution: 2→39.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 249116.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: This entry extends resolution from the previous 2.4A of PDB entry 1der to current 2.0A using the previous experimental data of 1der.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.3657 Å2 / ksol: 0.352588 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.2579 / Rfactor Rwork: 0.2428 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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