+Open data
-Basic information
Entry | Database: PDB / ID: 6nl1 | ||||||
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Title | Structure of T. brucei MERS1 protein in its apo form | ||||||
Components | Mitochondrial edited mRNA stability factor 1 | ||||||
Keywords | RNA BINDING PROTEIN / MERS1 / mRNA processing / nudix | ||||||
Function / homology | NUDIX domain / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Mitochondrial edited mRNA stability factor 1 Function and homology information | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.297 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Rna / Year: 2020 Title: Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inTrypanosoma brucei. Authors: Schumacher, M.A. / Henderson, M. / Zeng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nl1.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nl1.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nl1 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nl1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44714.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MERS1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SBM0 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 4.1 Å3/Da / Density % sol: 69.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Magnesium sulphate, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→49.975 Å / Num. obs: 33970 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.997 / Rpim(I) all: 0.028 / Rsym value: 0.45 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.2975→2.356 Å / CC1/2: 0.879 / Rpim(I) all: 0.278 / Rsym value: 0.345 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.297→49.975 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.03
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 48.741 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 155.59 Å2 / Biso mean: 40.14 Å2 / Biso min: 15.83 Å2
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Refinement step | Cycle: final / Resolution: 2.297→49.975 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 61.3837 Å / Origin y: -15.6503 Å / Origin z: 16.1326 Å
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Refinement TLS group |
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