+Open data
-Basic information
Entry | Database: PDB / ID: 3tut | ||||||
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Title | Crystal structure of RtcA.ATP binary complex | ||||||
Components | RNA 3'-terminal phosphate cyclase | ||||||
Keywords | TRANSFERASE / Cyclase family / Cyclization of RNA 3'-phosphate ends | ||||||
Function / homology | Function and homology information RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Chakravarty, A.K. / Smith, P. / Shuman, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis. Authors: Chakravarty, A.K. / Smith, P. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tut.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tut.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tut_validation.pdf.gz | 803.9 KB | Display | wwPDB validaton report |
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Full document | 3tut_full_validation.pdf.gz | 809.9 KB | Display | |
Data in XML | 3tut_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3tut_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/3tut ftp://data.pdbj.org/pub/pdb/validation_reports/tu/3tut | HTTPS FTP |
-Related structure data
Related structure data | 3tuxC 3tv1C 3tw3C 3kgdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38304.527 Da / Num. of mol.: 1 / Mutation: C308S, H309N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4475, JW5688, rtcA, yhgJ, yhgK / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP) |
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-Non-polymers , 5 types, 296 molecules
#2: Chemical | ChemComp-ATP / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG5000-MME, Ammonium sulfate, MES pH 6.5, ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9499 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9499 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→35.49 Å / Num. all: 41658 / Num. obs: 41491 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.9 Å2 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.58→1.67 Å / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KGD Resolution: 1.58→35.488 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 25.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.126 Å2 / ksol: 0.392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.58→35.488 Å
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Refine LS restraints |
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LS refinement shell |
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