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Yorodumi- PDB-2cjb: Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cjb | ||||||
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Title | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with serine | ||||||
Components | SERYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / TRNA SYNTHETASE / ZINC ION / SERINE | ||||||
Function / homology | Function and homology information selenocysteine biosynthetic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | METHANOSARCINA BARKERI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Bilokapic, S. / Maier, T. / Ahel, D. / Gruic-Sovulj, I. / Soll, D. / Weygand-Durasevic, I. / Ban, N. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition Authors: Bilokapic, S. / Maier, T. / Ahel, D. / Gruic-Sovulj, I. / Soll, D. / Weygand-Durasevic, I. / Ban, N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cjb.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cjb.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cjb ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cjb | HTTPS FTP |
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-Related 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: 60076.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ZINC ION IN ACTIVE SITE / Source: (gene. exp.) METHANOSARCINA BARKERI (archaea) / Strain: FUSARO / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q46AN5, serine-tRNA ligase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | HIS-TAG FROM PET15B PLASMID AT THE N-TERMINUS OF SERYL- TRNA SYNTHETASE | |
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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: 3.26 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: PROTEIN WAS CRYSTALLIZED FROM 5-9% MPD, 50 MM MES, PH 5.9, 294 K, HANGING DROP VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9782 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 39994 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→19.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 29.265 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.663 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→19.94 Å
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