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Yorodumi- PDB-4oi1: Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oi1 | ||||||
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Title | Clp1 bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set II) | ||||||
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: 2.3 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 | 4oi1.cif.gz | 175 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oi1.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 4oi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oi1 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oi1 | HTTPS FTP |
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-Related structure data
Related structure data | 4ohvC 4ohwC 4ohxC 4ohyC 4ohzC 4oi0C 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 , 5 types, 132 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ALF / |
#6: Chemical | ChemComp-2PE / |
#7: 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: 49.57 % Description: Deby-Scherrer rings at 3.62 Angstrom and 2.25 Angstrom resolution from salt in the cryo solution have been excluded during processing of the diffraction images from 3.65 Angstrom to 3.60 ...Description: Deby-Scherrer rings at 3.62 Angstrom and 2.25 Angstrom resolution from salt in the cryo solution have been excluded during processing of the diffraction images from 3.65 Angstrom to 3.60 Angstrom resolution and truncation to 2.3 Angstrom resolution). 4OI0 includes all data processed to 2.2 Angstrom resolution. |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / 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: 2.3→50 Å / Num. obs: 19865 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 38.4 Å2 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.5 % / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→36.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.628 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.24 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.278 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→36.66 Å
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Refine LS restraints |
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