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Yorodumi- PDB-4oi0: bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oi0 | ||||||
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Title | bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I) | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / polynucleotide kinase / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / : / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Dikfidan, A. / Loll, B. / Zeymer, C. / Clausen, T. / Meinhart, A. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1. Authors: Dikfidan, A. / Loll, B. / Zeymer, C. / Magler, I. / Clausen, T. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oi0.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oi0.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 4oi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oi0 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oi0 | HTTPS FTP |
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-Related structure data
Related structure data | 4ohvC 4ohwC 4ohxC 4ohyC 4ohzC 4oi1C 4oi2C 4oi4C 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
-Protein / RNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 47936.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: clpf-1, F59A2.4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P52874 |
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#2: RNA chain | Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized |
-Non-polymers , 6 types, 141 molecules
#3: Chemical | ChemComp-ADP / | ||||
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#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | ChemComp-ALF / | ||||
#6: Chemical | #7: Chemical | ChemComp-2PE / | #8: 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: 2.44 Å3/Da / Density % sol: 49.52 % Description: Diffraction data include Deby-Scherrer rings at 3.62 Angstrom and 2.25 Angstrom resolution from salt in the cryo solution |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Na2HPO4/KH2PO4 200 mM NaCl 15 mM MgCl2 90 mM sarcosine 25% (w/v) PEG 1000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2010 / Details: Rigaku VariMax |
Radiation | Monochromator: OSMIC KB MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 22553 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 36.8 Å2 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→36.66 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.481 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.251 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→36.66 Å
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Refine LS restraints |
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