+Open data
-Basic information
Entry | Database: PDB / ID: 1u7d | ||||||
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Title | crystal structure of apo M. jannashii tyrosyl-tRNA synthetase | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / Rossmann fold | ||||||
Function / homology | Function and homology information tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Zhang, Y. / Wang, L. / Schultz, P.G. / Wilson, I.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine. Authors: Zhang, Y. / Wang, L. / Schultz, P.G. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u7d.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u7d.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 1u7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/1u7d ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u7d | HTTPS FTP |
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-Related structure data
Related structure data | 1u7xC 1j1uS S: Starting model for refinement C: citing same article (ref.) |
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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: 35102.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: tyrS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q57834, tyrosine-tRNA ligase #2: 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: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 277 K / Method: liquid diffusion / pH: 5.5 Details: 12-15% PEG4000, 0.2M ammonium sulfate, 0.2M sodium acetate, , pH 5.5, LIQUID DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2002 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→47 Å / Num. all: 23781 / Num. obs: 22575 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 3.12 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1487 / Rsym value: 0.537 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1j1u Resolution: 2.65→41.68 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 58.37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→41.68 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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