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- PDB-3a7r: Crystal structure of E. coli lipoate-protein ligase A in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a7r | ||||||
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Title | Crystal structure of E. coli lipoate-protein ligase A in complex with lipoyl-AMP. | ||||||
![]() | Lipoate-protein ligase A | ||||||
![]() | LIGASE / ADENYLATE-FORMING ENZYME / lipoic acid / ATP-binding / Cytoplasm / Nucleotide-binding / Transferase / Lipoyl | ||||||
Function / homology | ![]() lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / protein lipoylation / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujiwara, K. / Hosaka, H. | ||||||
![]() | ![]() Title: Global conformational change associated with the two-step reaction catalyzed by Escherichia coli lipoate-protein ligase A. Authors: Fujiwara, K. / Maita, N. / Hosaka, H. / Okamura-Ikeda, K. / Nakagawa, A. / Taniguchi, H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.8 KB | Display | ![]() |
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Full document | ![]() | 738.1 KB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a7aC ![]() 3a7lC ![]() 3a7uC ![]() 2e5aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 37840.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32099, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases | ||||
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#2: Chemical | ChemComp-LAQ / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.6M Li2SO4, 0.01M MgSO4, 0.05M cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 44005 / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 8.2 / Num. unique all: 4299 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2E5A Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.442 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.328 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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