+Open data
-Basic information
Entry | Database: PDB / ID: 1li5 | ||||||
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Title | Crystal Structure of Cysteinyl-tRNA Synthetase | ||||||
Components | CYSTEINYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / TRNA SYNTHETASE / CYSTEINE / E.COLI | ||||||
Function / homology | Function and homology information cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / aminoacyl-tRNA ligase activity / ligase activity / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Newberry, K.J. / Hou, Y.-M. / Perona, J.J. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase Authors: Newberry, K.J. / Hou, Y.-M. / Perona, J.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary Diffraction Analysis of Escherichia Coli Cysteinyl-tRNA Synthetase Authors: Newberry, K.J. / Kohn, J. / Hou, Y.-M. / Perona, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1li5.cif.gz | 157.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1li5.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 1li5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1li5_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 1li5_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 1li5_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1li5_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/1li5 ftp://data.pdbj.org/pub/pdb/validation_reports/li/1li5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The active biological unit is a monomer |
-Components
#1: Protein | Mass: 52271.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P21888, cysteine-tRNA ligase #2: Chemical | #3: 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: 2.45 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 8000, 200 MM magnesium acetate, 1MM DTT, cacodylate, 5MM ATP, 10MM cysteine. 100 MM BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 13, 2001 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45 Å / Num. all: 46671 / Num. obs: 45949 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Num. unique all: 6494 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 45 Å |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2449639.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.9212 Å2 / ksol: 0.325178 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.245 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2758 |