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- PDB-2yxb: Crystal structure of the methylmalonyl-CoA mutase alpha-subunit f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yxb | ||||||
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Title | Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix | ||||||
![]() | Coenzyme B12-dependent mutase | ||||||
![]() | ISOMERASE / alpha/beta / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Handa, N. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix Authors: Handa, N. / Bessho, Y. / Yokoyama, 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 | ![]() | 37.7 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.1 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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Unit cell |
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Components
#1: Protein | Mass: 17982.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.662207 Å3/Da / Density % sol: 26.00201 % |
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Crystal grow | Temperature: 293 K / Method: oil batch Details: 0.4M Ammonium dihydrogen phosphate, oil batch, 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 15, 2006 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 11582 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.067 / Net I/σ(I): 17.8 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.35 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.745 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20 /
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