[English] 日本語
Yorodumi- PDB-5h4v: Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h4v | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae | ||||||
Components | Glutamate--tRNA ligase | ||||||
Keywords | LIGASE / Glutamyl-tRNA aminoacylation / ATP binding / Nucleotide binding | ||||||
Function / homology | Function and homology information glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xanthomonas oryzae pv. oryzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Doan, T.-N.-T. / Ho, T.-H. / Kang, L.-W. | ||||||
Citation | Journal: CROP PASTURE SCI / Year: 2017 Title: Transcriptional expression of aminoacyl tRNA synthetase genes of Xanthomonas oryzae pv. oryzae (Xoo) on rice-leaf extract treatment and crystal structure of Xoo glutamyl-tRNA synthetase Authors: Ho, T.-H. / Hong, M.-K. / Kim, S. / Kim, J.-G. / Lee, J. / Jung, K. / Lee, I. / Choi, M. / Park, H. / Lee, S. / Ahn, Y.-J. / Kang, L.-W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h4v.cif.gz | 526.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h4v.ent.gz | 435.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/5h4v ftp://data.pdbj.org/pub/pdb/validation_reports/h4/5h4v | HTTPS FTP |
---|
-Related structure data
Related structure data | 2cfoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54181.434 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) (bacteria) Strain: KACC10331 / KXO85 / Gene: gltX, XOO1504 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q5H2R3, glutamate-tRNA ligase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 55%(v/v) Tacsimate, 0.1M bistris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2008 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 59553 / % possible obs: 90.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.8 / % possible all: 65.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CFO Resolution: 3→29.44 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.863 / SU B: 27.205 / SU ML: 0.478 / Cross valid method: THROUGHOUT / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 70.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→29.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|