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Yorodumi- PDB-4v43: Structural and mechanistic basis for allostery in the bacterial c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v43 | |||||||||
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Title | Structural and mechanistic basis for allostery in the bacterial chaperonin GroEL | |||||||||
Components | GROEL PROTEINGroEL | |||||||||
Keywords | CHAPERONE / Wild Type GroEL / ALLOSTERY | |||||||||
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 / response to heat ...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 / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å | |||||||||
Authors | Wang, J. | |||||||||
Citation | Journal: To be Published Title: A GroEL/GroES complex structure revisited: the structure-based mechanism of ATP hydrolysis 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 | 4v43.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v43.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v43 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v43 | HTTPS FTP |
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-Related structure data
Related structure data | 1kp8S 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: 57158.457 Da / Num. of mol.: 28 / Mutation: D398A 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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.25 % |
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Crystal grow | pH: 7 / Details: pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Detector: CCD / Date: Nov 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. obs: 217987 / % possible obs: 85.1 % / Observed criterion σ(I): -3 / Redundancy: 11.02 % / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 3.5→3.62 Å / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 1.396 / % possible all: 51.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kp8 Resolution: 3.52→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.4049 Å2 / ksol: 0.231794 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 80.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.52→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.52→3.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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