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Yorodumi- PDB-4h2t: Crystal structure of Bradyrhizobium japonicum glycine:[carrier pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h2t | ||||||
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Title | Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and an analogue of glycyl adenylate | ||||||
Components |
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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: 2.44 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h2t.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h2t.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h2t_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4h2t_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4h2t_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 4h2t_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h2t ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h2t | HTTPS FTP |
-Related structure data
Related structure data | 4h2sC 4h2uC 4h2vC 4h2wC 4h2xC 4h2yC 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
-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 |
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-Non-polymers , 5 types, 223 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 48.94 % |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 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: 0.95373 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→46.49 Å / Num. all: 36794 / Num. obs: 36621 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 43.465 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 46.49 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.44→46.49 Å / Occupancy max: 1 / Occupancy min: 0.13 / SU ML: 0.28 / σ(F): 1.99 / Phase error: 20.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.71 Å2 / Biso mean: 29.6736 Å2 / Biso min: 2.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→46.49 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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