[English] 日本語
Yorodumi- PDB-4h2u: Crystal structure of Bradyrhizobium japonicum glycine:[carrier pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h2u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and ATP | ||||||
Components |
| ||||||
Keywords | LIGASE / ATP binding / glycine binding / carrier protein / aminoacyl-tRNA synthetase / seryl-tRNA synthetase. | ||||||
Function / homology | Function and homology information : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / lipid A biosynthetic process / acyl binding / acyl carrier activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Luic, M. / Weygand-Durasevic, I. / Ivic, N. / Mocibob, M. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation. Authors: Mocibob, M. / Ivic, N. / Luic, M. / Weygand-Durasevic, I. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Homologs of aminoacyl-tRNA synthetases acylate carrier proteins and provide a link between ribosomal and nonribosomal peptide synthesis Authors: Mocibob, M. / Ivic, N. / Bilokapic, S. / Maier, T. / Luic, M. / Ban, N. / Weygand-Durasevic, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4h2u.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4h2u.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h2u_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4h2u_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4h2u_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 4h2u_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h2u ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h2u | HTTPS FTP |
-Related structure data
Related structure data | 4h2sC 4h2tC 4h2vC 4h2wC 4h2xC 4h2yC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 38159.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bll0957 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q89VT8, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases #2: Protein | Mass: 12116.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Gene: bsr0959 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89VT6 |
---|
-Non-polymers , 7 types, 349 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-ACT / | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25.5% PEG 8000, 0.17M ammonium sulfate, 0.085 M sodium cacodylate pH 6.5, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 26, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→46.32 Å / Num. all: 57678 / Num. obs: 56605 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 39.065 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.41 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→46.32 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.2 / σ(F): 1.99 / Phase error: 19.97 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.64 Å2 / Biso mean: 36.5416 Å2 / Biso min: 9.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.32 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|