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Yorodumi- PDB-3pzc: Crystal structure of class II aaRS homologue (Bll0957) complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pzc | ||||||
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Title | Crystal structure of class II aaRS homologue (Bll0957) complexed with Coenzyme A | ||||||
Components | Amino acid--[acyl-carrier-protein] ligase 1 | ||||||
Keywords | LIGASE / amino acid:[carrier protein] ligase / seryl-tRNA synthetase / carrier protein / Coenzyme A | ||||||
Function / homology | Function and homology information : / aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bradyrhizobium japonicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Weygand-Durasevic, I. / Luic, M. / Mocibob, M. / Ivic, N. / Subasic, D. | ||||||
Citation | Journal: Croatica Chemica Acta / Year: 2011 Title: Substrate Recognition by Novel Family of Amino Acid:[Carrier Protein] Ligases Authors: Mocibob, M. / Ivic, N. / Subasic, D. / 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 | 3pzc.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pzc.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 3pzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pzc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3pzc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3pzc_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 3pzc_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pzc ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pzc | HTTPS FTP |
-Related structure data
Related structure data | |
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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 , 1 types, 2 molecules AB
#1: Protein | Mass: 38159.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: bll0957 / Production host: Escherichia coli (E. coli) References: UniProt: Q89VT8, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases |
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-Non-polymers , 6 types, 331 molecules
#2: Chemical | #3: Chemical | ChemComp-GAP / | #4: Chemical | #5: Chemical | ChemComp-COA / | #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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.17M ammonium acetate, 0.085M sodium acetate trihydrate, 25.5% PEG 4000, 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: OXFORD RUBY CCD / Detector: CCD / Date: Jan 28, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Nova optical assembly incorporating graded multilayer optics Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→20.86 Å / Num. all: 34431 / Num. obs: 32404 / % possible obs: 99.85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.95 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.6755 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→20.86 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 1.88 / σ(F): 0.01 / 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 / Bsol: 49.832 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.64 Å2 / Biso mean: 26.3009 Å2 / Biso min: 4.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20.86 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: 11
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