+Open data
-Basic information
Entry | Database: PDB / ID: 1mnf | ||||||
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Title | Domain motions in GroEL upon binding of an oligopeptide | ||||||
Components |
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Keywords | CHAPERONE / GROEL / FORCED UNFOLDING / DOMAIN MOTIONS / OPPOSITE ALLOSTERIC | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Wang, J. / Chen, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Domain Motions in GroEL upon Binding of an Oligopeptide. Authors: Wang, J. / Chen, L. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: The Crystal Structure of a Groel/Peptide Complex: Plasticity as a Basis for Substrate Diversity Authors: Chen, L. / Sigler, P.B. #2: 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. #3: 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. #4: 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. #5: 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 | 1mnf.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1mnf.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1mnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mnf_validation.pdf.gz | 593.4 KB | Display | wwPDB validaton report |
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Full document | 1mnf_full_validation.pdf.gz | 785.4 KB | Display | |
Data in XML | 1mnf_validation.xml.gz | 259.4 KB | Display | |
Data in CIF | 1mnf_validation.cif.gz | 346.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mnf ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mnf | 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: 57260.504 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5 #2: Protein/peptide | Mass: 1460.676 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.75 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 7 / Details: PEG, pH 7, VAPOR DIFFUSION, temperature 300K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 28 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Boisvert, D.C., (1996) Nat.Struct.Biol., 3, 170. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 167654 / % possible obs: 84.4 % / Num. measured all: 436111 / Rmerge(I) obs: 0.099 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.2 Å / % possible obs: 73.9 % / Rmerge(I) obs: 0.147 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20.01 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 16.633 Å2 / ksol: 0.326259 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.42 Å / Luzzati sigma a free: 0.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.2 Å |