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Yorodumi- PDB-4yrq: Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yrq | ||||||
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Title | Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 6-amino-2H-chromen-2-one (Chem 744) | ||||||
Components | Histidyl-tRNA synthetase | ||||||
Keywords | Ligase/Ligase inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / HisRS / Trypanosoma cruzi / protein-inhibitor complex / Ligase-Ligase inhibitor complex | ||||||
Function / homology | Function and homology information histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Koh, C.-Y. / Hol, W.G.J. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015 Title: A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens. Authors: Koh, C.Y. / Siddaramaiah, L.K. / Ranade, R.M. / Nguyen, J. / Jian, T. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yrq.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yrq.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yrq_validation.pdf.gz | 482 KB | Display | wwPDB validaton report |
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Full document | 4yrq_full_validation.pdf.gz | 483.3 KB | Display | |
Data in XML | 4yrq_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 4yrq_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/4yrq ftp://data.pdbj.org/pub/pdb/validation_reports/yr/4yrq | HTTPS FTP |
-Related structure data
Related structure data | 4yp0C 4ypfC 4yrcC 4yreC 4yrfC 4yrgC 4yriC 4yrjC 4yrkC 4yrlC 4yrmC 4yrnC 4yroC 4yrpC 4yrrC 4yrsC 4yrtC 3lc0S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51185.590 Da / Num. of mol.: 1 / Fragment: UNP residues 45-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053507019.40 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DA54, histidine-tRNA ligase |
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-Non-polymers , 6 types, 209 molecules
#2: Chemical | ChemComp-HIS / | ||||
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#3: Chemical | ChemComp-4JQ / | ||||
#4: Chemical | ChemComp-EDO / | ||||
#5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: 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: 2.51 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP PH range: 4.8 to 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 20, 2013 | |||||||||||||||||||||||||||
Radiation | Monochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.05→27.82 Å / Num. obs: 31011 / % possible obs: 98.2 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Net I/σ(I): 10.6 / Num. measured all: 87563 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LC0 Resolution: 2.05→27.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.604 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.36 Å2 / Biso mean: 39.798 Å2 / Biso min: 18.4 Å2
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Refinement step | Cycle: final / Resolution: 2.05→27.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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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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