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- PDB-2cxh: Crystal structure of probable ribosomal biogenesis protein from A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cxh | ||||||
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Title | Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1 | ||||||
![]() | Probable brix-domain ribosomal biogenesis protein | ||||||
![]() | RNA BINDING PROTEIN / BRIX domain / 18S rRNA / IMP4 / U3 snoRNP / ribosomal biogenesis / RNA-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawazoe, M. / Takemoto, C. / Hanawa-Suetsugu, K. / Kaminishi, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1 Authors: Kawazoe, M. / Takemoto, C. / Hanawa-Suetsugu, K. / Kaminishi, T. / Terada, T. / Shirouzu, M. / 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 | ![]() | 47.9 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.2 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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Unit cell |
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Components
#1: Protein | Mass: 23774.678 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: 2.26692 Å3/Da / Density % sol: 45.741364 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.01M Tris-HCl pH 8.0, 0.15M NaCl, 0.001M DTT, 0.05M tri-sodium citrate pH 5.6, 10% v/v 2-propanol, 10% w/v polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.697→37.796 Å / Num. obs: 22973 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 8.36835 % / Biso Wilson estimate: 11 Å2 / Rsym value: 0.09 / Net I/σ(I): 23.616 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 22973 / Rsym value: 0.608 / % possible all: 95.4 |
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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: 38.244 Å2 / ksol: 0.36566 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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