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Yorodumi- PDB-5x6c: Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x6c | ||||||
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Title | Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / O-phosphoseryl-tRNA synthetase / multiple domain protein / coiled-coil insertion | ||||||
Function / homology | Function and homology information O-phospho-L-serine-tRNA ligase / phosphoserine-tRNA(Cys) ligase activity / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å | ||||||
Authors | Chen, M. / Kato, K. / Yao, M. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis for tRNA-dependent cysteine biosynthesis Authors: Chen, M. / Kato, K. / Kubo, Y. / Tanaka, Y. / Liu, Y. / Long, F. / Whitman, W.B. / Lill, P. / Gatsogiannis, C. / Raunser, S. / Shimizu, N. / Shinoda, A. / Nakamura, A. / Tanaka, I. / Yao, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x6c.cif.gz | 246.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6c.ent.gz | 194.1 KB | Display | PDB format |
PDBx/mmJSON format | 5x6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6c ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6c | HTTPS FTP |
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-Related structure data
Related structure data | 5x6bC 2du7S 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: Protein | Mass: 63889.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Strain: DSM 2661 / Gene: MJ1660 / Production host: Escherichia coli (E. coli) References: UniProt: Q59054*PLUS, O-phospho-L-serine-tRNA ligase #2: Protein | Mass: 25334.650 Da / Num. of mol.: 2 / Fragment: UNP residues 1-24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1481 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58876 #3: Chemical | #4: Chemical | #5: 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: 5.12 Å3/Da / Density % sol: 82.41 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 0.1M Tris-HCl pH7.0, 0.3M Ammonium sulfate, 36% MPD PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48 Å / Num. obs: 65670 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DU7 Resolution: 3.101→47.989 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.101→47.989 Å
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Refine LS restraints |
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LS refinement shell |
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