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Yorodumi- PDB-3vz7: Crystal Structure Analysis of the mini-chaperonin variant with Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vz7 | ||||||
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Title | Crystal Structure Analysis of the mini-chaperonin variant with Pro 187 Gly | ||||||
Components | 60 kDa chaperonin | ||||||
Keywords | CHAPERONE / Chaperonin / HSP60 / GroEL / Cell division / ATP-binding / Phospholyration | ||||||
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: 1.8 Å | ||||||
Authors | Saijo, S. / Sato, T. | ||||||
Citation | Journal: To be Published Title: Binding Energy(BE) from Crystal Packing of Mini-chaperones (mcpn) Provided Insights into the Allosteric Interaction of GroEL/ES Complex Authors: Saijo, S. / Sato, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vz7.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vz7.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vz7_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 3vz7_full_validation.pdf.gz | 421.6 KB | Display | |
Data in XML | 3vz7_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3vz7_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/3vz7 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/3vz7 | HTTPS FTP |
-Related structure data
Related structure data | 3vz6C 3vz8C 1kidS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 21587.734 Da / Num. of mol.: 1 / Fragment: Apical domain, UNP residues 191-376 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6F5 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES 184-190 ARE HETEROLOGO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.07 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 0.1M Tris-HCl, 1M NaCl, 3.75% Glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 10, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 21847 / Num. obs: 21847 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 15.5 Å2 |
Reflection shell | Resolution: 1.8→1.91 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KID Resolution: 1.8→29.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1217562.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.3501 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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