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Yorodumi- PDB-3zxi: Crystal structure of human mitochondrial tyrosyl-tRNA synthetase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zxi | ||||||
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Title | Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog | ||||||
Components | TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN-SUBSTRATE COMPLEX / ATP-BINDING / PROTEIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation ...mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Bonnefond, L. / Frugier, M. / Rudinger-Thirion, J. / Balg, C. / Chenevert, R. / Lorber, B. / Giege, R. / Sauter, C. | ||||||
Citation | Journal: Cryst.Growth Des. / Year: 2011 Title: Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination Authors: Bonnefond, L. / Schellenberger, P. / Basquin, J. / Demangeat, G. / Ritzenthaler, C. / Chenevert, R. / Balg, C. / Frugier, M. / Rudinger-Thirion, J. / Giege, R. / Lorber, B. / Sauter, C. #1: Journal: Structure / Year: 2007 Title: Crystal Structure of Human Mitochondrial Tyrosyl- tRNA Synthetase Reveals Common and Idiosyncratic Features. Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zxi.cif.gz | 263.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zxi.ent.gz | 213.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxi ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxi | HTTPS FTP |
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-Related structure data
Related structure data | 2y90C 2yhtC 4v5wC 2pidS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 39962.371 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Y2Z4, tyrosine-tRNA ligase #2: Chemical | Sequence details | THE CONSTRUCT LACKS THE MITOCHONDR | |
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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: THE PROTEIN (20 MG/ML STOCK SOLUTION) WAS CRYSTALLIZED AT 293K BY VAPOR DIFFUSION (SITTING DROP) WITH A RESERVOIR SOLUTION CONTAINING 30% (M/V) PEG-4000, 0.1 M NA ACETATE PH 4.6, 0.2 M NH4 ...Details: THE PROTEIN (20 MG/ML STOCK SOLUTION) WAS CRYSTALLIZED AT 293K BY VAPOR DIFFUSION (SITTING DROP) WITH A RESERVOIR SOLUTION CONTAINING 30% (M/V) PEG-4000, 0.1 M NA ACETATE PH 4.6, 0.2 M NH4 ACETATE, 0.1 M TRIS-HCL PH 7.5, 1.2 M NA MALONATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 16741 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 65.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.46 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PID Resolution: 2.75→29.937 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.985 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→29.937 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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