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Yorodumi- PDB-4ohy: C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ohy | ||||||
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Title | C. Elegans Clp1 bound to ssRNA dinucleotide GC, AMP-PNP, and Mg2+(inhibited substrate bound state) | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / polynucleotide kinase / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information Processing of Capped Intron-Containing Pre-mRNA / Processing of Intronless Pre-mRNAs / ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / polynucleotide 5'-hydroxyl-kinase activity / mRNA cleavage factor complex / tRNA splicing, via endonucleolytic cleavage and ligation / mRNA 3'-end processing / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 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 | 4ohy.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ohy.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ohy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ohy_validation.pdf.gz | 1016 KB | Display | wwPDB validaton report |
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Full document | 4ohy_full_validation.pdf.gz | 1018.2 KB | Display | |
Data in XML | 4ohy_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4ohy_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/4ohy ftp://data.pdbj.org/pub/pdb/validation_reports/oh/4ohy | HTTPS FTP |
-Related structure data
Related structure data | 4ohvC 4ohwC 4ohxC 4ohzC 4oi0C 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 , 4 types, 152 molecules
#3: Chemical | ChemComp-ANP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-2PE / |
#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: 2.42 Å3/Da / Density % sol: 49.16 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 30691 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 42.1 Å2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.1 % / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→43.48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.228 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 36.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.48 Å
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Refine LS restraints |
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