+Open data
-Basic information
Entry | Database: PDB / ID: 5k78 | ||||||
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Title | Dbr1 in complex with 16-mer branched RNA | ||||||
Components |
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Keywords | HYDROLASE/RNA / metalloenzyme / complex / branched RNA / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information RNA lariat debranching enzyme activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / RNA splicing, via transesterification reactions / mRNA splicing, via spliceosome / manganese ion binding / iron ion binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.64 Å | ||||||
Authors | Clark, N.E. / Taylor, A.B. / Hart, P.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures Authors: Clark, N.E. / Katolik, A. / Roberts, K. / Taylor, A.B. / Holloway, S.P. / Schuermann, J.P. / Montemayor, E.J. / Stevens, S.W. / Fitzpatrick, P.F. / Damha, M.J. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k78.cif.gz | 748.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k78.ent.gz | 620.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k78_validation.pdf.gz | 529.4 KB | Display | wwPDB validaton report |
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Full document | 5k78_full_validation.pdf.gz | 544.5 KB | Display | |
Data in XML | 5k78_validation.xml.gz | 59.1 KB | Display | |
Data in CIF | 5k78_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k78 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k78 | HTTPS FTP |
-Related structure data
Related structure data | 5k71C 5k73C 4pefS 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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2 |
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5 |
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Unit cell |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 41846.934 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Production host: Escherichia coli (E. coli) / References: UniProt: C4M1P9 |
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-RNA chain , 2 types, 4 molecules XYxy
#2: RNA chain | Mass: 3475.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This is a branched RNA 5'-UACUAA(2'-GUAUG)CAAGU-3' / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #3: RNA chain | Mass: 1893.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This is a branched RNA 5'-UACUAA(2'-GUAUG)CAAGU-3' / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
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-Non-polymers , 4 types, 48 molecules
#4: Chemical | ChemComp-FE2 / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-SO4 / #7: 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: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, lithium sulfate, glycerol, bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.28081 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28081 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→108 Å / Num. obs: 66902 / % possible obs: 99.14 % / Redundancy: 5.6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.151 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.64→2.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.76 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4pef Resolution: 2.64→71.336 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 29.05 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→71.336 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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