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- PDB-3w6k: Crystal structure of dimer of ScpB N-terminal domain complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w6k | ||||||
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Title | Crystal structure of dimer of ScpB N-terminal domain complexed with ScpA peptide | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamada, K. / Hirano, T. | ||||||
![]() | ![]() Title: Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB Authors: Kamada, K. / Miyata, M. / Hirano, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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/peptide | Mass: 1996.222 Da / Num. of mol.: 2 / Fragment: UNP residues 125-142 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) ![]() ![]() ![]() #2: Protein | Mass: 9761.276 Da / Num. of mol.: 4 / Fragment: UNp residues 12-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: strain 10 / Gene: scpB / Plasmid: modified pET28a / Production host: ![]() ![]() ![]() #3: Water | ChemComp-HOH / | ![]() Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN ENTITY 2, GPHM HAVE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. IN ENTITY 2, GPHM HAVE BEEN ADDED AT N-TERMINAL. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.5 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 100mM Na malonate-HCl, 3.0-3.3M Na formate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.374→50 Å / Num. obs: 23087 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.586 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 37.406 |
Reflection shell | Resolution: 2.374→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 11.464 / Num. unique all: 1048 / Rsym value: 0.116 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Dimer of Geobacillus stearothermophilus ScpB N-terminal domain Resolution: 2.374→46.476 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.526 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.374→46.476 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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