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Yorodumi- PDB-1q11: Crystal structure of an active fragment of human tyrosyl-tRNA syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q11 | ||||||
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Title | Crystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol | ||||||
Components | Tyrosyl-tRNA synthetase | ||||||
Keywords | LIGASE / Rossmann fold domain containing the active site / anticodon recognition domain / substrate analog tyrosinol co-crystalized | ||||||
Function / homology | Function and homology information interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / RNA binding / extracellular space / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Yang, X.-L. / Schimmel, P. / Ribas de Pouplana, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains Authors: Yang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P. / Ribas De Pouplana, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q11.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q11.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 1q11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q11_validation.pdf.gz | 469.7 KB | Display | wwPDB validaton report |
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Full document | 1q11_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | 1q11_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1q11_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q11 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q11 | HTTPS FTP |
-Related structure data
Related structure data | 1r6tC 1n3lS 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 on special symmetry positions |
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Details | asymmetric unit contains a monomer of the biologically dimer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase |
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-Non-polymers , 5 types, 353 molecules
#2: Chemical | ChemComp-PO4 / | ||
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#3: Chemical | ChemComp-K / | ||
#4: Chemical | ChemComp-TYE / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: (NH4)2SO4, NAH2PO4, K2HPO4, ACETONE, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X26C / Wavelength: 1.28 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 58862 / Num. obs: 53993 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.301 / % possible all: 64.5 |
Reflection | *PLUS Num. obs: 55381 / % possible obs: 93.8 % / Redundancy: 6.7 % |
Reflection shell | *PLUS % possible obs: 64.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N3L, mini TyrRS alone Resolution: 1.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |