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- PDB-2ywx: Crystal structure of phosphoribosylaminoimidazole carboxylase cat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ywx | ||||||
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Title | Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii | ||||||
![]() | Phosphoribosylaminoimidazole carboxylase catalytic subunit | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii Authors: Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.3 KB | Display | ![]() |
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PDB format | ![]() | 29.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1o4vS S: Starting model for refinement |
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Similar structure data | |
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: 16974.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pET-21a / Production host: ![]() ![]() ![]() References: UniProt: Q58033, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 0.1M Natrium Acetate(pH 4.4), 3.2M Natrium Chloride, 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: Mar 18, 2007 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.31→50 Å / Num. obs: 8318 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.415 / Num. unique all: 1545 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1O4V Resolution: 2.31→31.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 509961.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.2955 Å2 / ksol: 0.351168 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→31.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.45 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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