+Open data
-Basic information
Entry | Database: PDB / ID: 3k80 | ||||||
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Title | Structure of essential protein from Trypanosoma brucei | ||||||
Components |
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Keywords | Immune System / RNA Binding Protein / RNA-editing / OB-fold / RNA-binding proteins | ||||||
Function / homology | Function and homology information RNA modification / mitochondrial mRNA editing complex / kinetoplast / single-stranded DNA binding / endonuclease activity / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | Lama glama (llama) Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wu, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies. Authors: Wu, M. / Park, Y.J. / Pardon, E. / Turley, S. / Hayhurst, A. / Deng, J. / Steyaert, J. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k80.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k80.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/3k80 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/3k80 | HTTPS FTP |
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-Related structure data
Related structure data | 3k7uC 3k81C 1eqqS 1i3vS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Antibody | Mass: 14130.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 16119.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.70.2090 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38B90 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG4000, 10% iso-propanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 13, 2009 |
Radiation | Monochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 21647 / % possible obs: 92.6 % / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Biso Wilson estimate: 64.3 Å2 / Rsym value: 0.068 / Net I/σ(I): 37 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 21647 / Rsym value: 0.62 / % possible all: 60.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EQQ for chain C&D and 1I3V for chain A&B Resolution: 2.4→27.801 Å / SU ML: 0.43 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.354 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.801 Å
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Refine LS restraints |
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LS refinement shell |
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