+Open data
-Basic information
Entry | Database: PDB / ID: 5cot | ||||||
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Title | Structure and mechanism of a eukaryal nick-sealing RNA ligase | ||||||
Components | Naegleria gruberi RNA ligase | ||||||
Keywords | LIGASE / RNA repair / adenylyltransferase | ||||||
Function / homology | RNA ligase, DRB0094 / PHA02142 OB-fold domain / RNA ligase domain, REL/Rln2 / RNA ligase / ATP binding / metal ion binding / ADENOSINE MONOPHOSPHATE / Predicted protein Function and homology information | ||||||
Biological species | Naegleria gruberi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å | ||||||
Authors | Unciuleac, M.C. / Goldgur, Y. / Shuman, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase. Authors: Unciuleac, M.C. / Goldgur, Y. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cot.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cot.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cot_validation.pdf.gz | 790.1 KB | Display | wwPDB validaton report |
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Full document | 5cot_full_validation.pdf.gz | 793.8 KB | Display | |
Data in XML | 5cot_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5cot_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/5cot ftp://data.pdbj.org/pub/pdb/validation_reports/co/5cot | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38661.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_82186 / Production host: Escherichia coli (E. coli) / References: UniProt: D2W2Z5 |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 30% PEG 6000 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→20 Å / Num. obs: 38947 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.51 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.69→19.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.265 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.614 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→19.61 Å
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Refine LS restraints |
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