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Yorodumi- PDB-1x2h: Crystal Structure of Lipate-Protein Ligase A from Escherichia col... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x2h | ||||||
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Title | Crystal Structure of Lipate-Protein Ligase A from Escherichia coli complexed with lipoic acid | ||||||
Components | Lipoate-protein ligase ALipoate–protein ligase | ||||||
Keywords | LIGASE / lipoate-protein ligase / lipoic acid / protein acylation / post-translational modification | ||||||
Function / homology | Function and homology information lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 2.91 Å | ||||||
Authors | Fujiwara, K. / Toma, S. / Okamura-Ikeda, K. / Motokawa, Y. / Nakagawa, A. / Taniguchi, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of lipoate-protein ligase A from Escherichia coli: Determination of the lipoic acid-binding site Authors: Fujiwara, K. / Toma, S. / Okamura-Ikeda, K. / Motokawa, Y. / Nakagawa, A. / Taniguchi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x2h.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x2h.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/1x2h ftp://data.pdbj.org/pub/pdb/validation_reports/x2/1x2h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 38075.098 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS References: UniProt: P32099, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: 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: 3 Å3/Da / Density % sol: 58.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ethylene glycol, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.92154 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Feb 7, 2004 / Details: mirror |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92154 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→200 Å / Num. all: 29247 / Num. obs: 29247 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2939 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier Starting model: Lipoate protein ligase A from E. coli Resolution: 2.91→66.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.859 / SU B: 15.864 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 39.469 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→66.67 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.91 Å / Num. reflection Rwork: 1955 / Total num. of bins used: 20 |