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- PDB-3a7a: 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: 3a7a | ||||||
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Title | Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein | ||||||
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![]() | LIGASE / ADENIYLATE-FORMING ENZYME / ATP-binding / Nucleotide-binding / Transferase / Lipoyl | ||||||
Function / homology | ![]() lipoyltransferase activity / lipoate-protein ligase / lipoate-protein ligase activity / glycine cleavage complex / glycine decarboxylation via glycine cleavage system / protein lipoylation / one-carbon metabolic process / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujiwara, K. / Hosaka, H. / Nakagawa, A. | ||||||
![]() | ![]() 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 | ![]() | 187.1 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a7lC ![]() 3a7rC ![]() 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37840.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32099, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases #2: Protein | Mass: 13688.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16.2% PEG 3350, 0.045M MgSO4, 0.045M NaCl, 1mM NiCl2, 2% Polyethylene glycol monomethyl ether 2000, 0.01M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Mar 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→50 Å / Num. obs: 23803 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E5A Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.909 / SU ML: 0.433 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.457 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.179 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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