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Yorodumi- PDB-4h2w: Crystal structure of engineered Bradyrhizobium japonicum glycine:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h2w | ||||||
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Title | Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and AMP | ||||||
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 / ligase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) Agrobacterium fabrum (bacteria) Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 | 4h2w.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h2w.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h2w_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4h2w_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4h2w_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 4h2w_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/4h2w ftp://data.pdbj.org/pub/pdb/validation_reports/h2/4h2w | HTTPS FTP |
-Related structure data
Related structure data | 4h2sC 4h2tC 4h2uC 4h2vC 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: 38173.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria), (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: USDA 110 / Gene: bll0957, Atu2573,AGR_C_4663 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q89VT8, UniProt: Q7CWR3, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases #2: Protein | Mass: 11165.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4658, Atu2571 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CHM9 |
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-Non-polymers , 6 types, 377 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-5GP / | #6: Chemical | ChemComp-AMP / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAINS A, B ARE CHIMERIC PROTEINS COMPOSED OF UNP RESIDUES Q89VT8 1-220, Q7CWR3 236-246, Q89VT8 232-326 |
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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: 2.63 Å3/Da / Density % sol: 53.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10% PEG 4000, 10% PEG 8000, 0.17M ammonium acetate, 0.085M trisodium citrate dyhydrate pH 5.6, 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: 0.95372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 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: 1.94→45.755 Å / Num. all: 76863 / Num. obs: 76787 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 33.426 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.755 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.16 / σ(F): 1.99 / Phase error: 18.17 / 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: 124.58 Å2 / Biso mean: 33.1615 Å2 / Biso min: 7.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.755 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: 27
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