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- PDB-7c4c: The crystal structure of Trypanosoma brucei RNase D : GMP complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c4c | ||||||
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Title | The crystal structure of Trypanosoma brucei RNase D : GMP complex | ||||||
![]() | CCHC-type domain-containing protein | ||||||
![]() | RNA BINDING PROTEIN / Trypanosoma brucei / RNase D / guide RNA degradation / GMP | ||||||
Function / homology | ![]() PET complex / nucleobase-containing compound metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / nucleotide binding / mitochondrion / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, Y.Q. / Gan, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei. Authors: Gao, Y. / Liu, H. / Zhang, C. / Su, S. / Chen, Y. / Chen, X. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Li, J. / Huang, Z. / Ma, J. / Gan, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.4 KB | Display | ![]() |
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PDB format | ![]() | 118.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.5 MB | Display | ![]() |
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Full document | ![]() | 5.5 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 38986.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3670 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-5GP / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→30.15 Å / Num. obs: 20606 / % possible obs: 98.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.032 / Rrim(I) all: 0.095 / Χ2: 0.903 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.69 Å2 / Biso mean: 41.8257 Å2 / Biso min: 13.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.265→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -17.2869 Å / Origin y: 8.6059 Å / Origin z: -12.4793 Å
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Refinement TLS group | Selection details: all |