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Open data
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Basic information
Entry | Database: PDB / ID: 4ohx | ||||||
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Title | C. Elegans Clp1 bound to ADP and Mg2+ (RNA released state) | ||||||
![]() | Protein clpf-1 | ||||||
![]() | RNA BINDING PROTEIN / polynucleotide kinase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dikfidan, A. / Loll, B. / Zeymer, C. / Clausen, T. / Meinhart, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179 KB | Display | ![]() |
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PDB format | ![]() | 140.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ohvC ![]() 4ohwC ![]() 4ohyC ![]() 4ohzC ![]() 4oi0C ![]() 4oi1C ![]() 4oi2C ![]() 4oi4C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47936.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-2PE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 30056 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.8 Å2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.5 % / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 34.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→42.84 Å
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Refine LS restraints |
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