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- PDB-4o8j: Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o8j | ||||||
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Title | Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii, in complex with rACAAA3'phosphate and adenine. | ||||||
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![]() | Ligase/RNA / 3' RNA Cyclase / RNA / Ligase-RNA complex | ||||||
Function / homology | ![]() RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Desai, K.K. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T. | ||||||
![]() | ![]() Title: Structure of RNA 3'-phosphate cyclase bound to substrate RNA. Authors: Desai, K.K. / Bingman, C.A. / Cheng, C.L. / Phillips Jr., G.N. / Raines, R.T. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281.9 KB | Display | ![]() |
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PDB format | ![]() | 229.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4o89SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37221.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH1529, PHCV028, rtcA / Production host: ![]() ![]() References: UniProt: O59198, RNA 3'-terminal-phosphate cyclase (ATP) #2: RNA chain | Mass: 1906.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M proline, 0.1 M HEPES pH 7.5, 10% PEG 3350, cryoprotected by supplementing with 30% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2013 |
Radiation | Monochromator: Dual silicon, K-B mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 75635 / Num. obs: 75619 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % |
Reflection shell | Resolution: 2.04→2.08 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4O89 Resolution: 2.04→46.14 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→46.14 Å
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Refine LS restraints |
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LS refinement shell |
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