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- PDB-2cwl: Crystal structure of manganese-free form of pseudocatalase from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cwl | ||||||
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Title | Crystal structure of manganese-free form of pseudocatalase from Thermus thermophilus HB8 | ||||||
![]() | manganese-free pseudocatalase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Manganese catalase / Manganese catalase, ferritin-like di-iron-binding domain / Manganese containing catalase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / Manganese-containing pseudocatalase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural and functional analysis of pseudocatalase from Thermus thermophilus HB8 Authors: Ebihara, A. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.5 KB | Display | ![]() |
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PDB format | ![]() | 103.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.6 KB | Display | ![]() |
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Full document | ![]() | 423.8 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33373.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 40% PEG400, 0.1M Tris-HCl, 0.25M Li sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2004 |
Radiation | Monochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→46.44 Å / Num. obs: 90305 / % possible obs: 99.8 % / Redundancy: 19.14 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 9.36 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.3765 Å2 / ksol: 0.400672 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→43.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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