[English] 日本語
Yorodumi- PDB-2cja: Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cja | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP | ||||||
Components | SERYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / ZINC ION / TRNA SYNTHETASE | ||||||
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: 2.2 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cja.cif.gz | 214.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cja.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cja ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cja | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60779.902 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 |
---|
-Non-polymers , 5 types, 460 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | HIS-TAG FROM PET15B PLASMID AT THE N-TERMINUS OF SERYL- TRNA SYNTHETASE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.4 % |
---|---|
Crystal grow | pH: 5.9 / Details: pH 5.90 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9784 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 75693 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.2→19.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.09 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|