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- PDB-5ig8: Crystal structure of macrocyclase MdnB from Microcystis aeruginosa MRC -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ig8 | ||||||
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Title | Crystal structure of macrocyclase MdnB from Microcystis aeruginosa MRC | ||||||
![]() | ATP grasp ligase | ||||||
![]() | LIGASE / RiPP / Macrocyclase | ||||||
Function / homology | ATP-grasp ribosomal peptide maturase, MvdC family / ligase activity / ATP grasp ligase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, K. / Condurso, H.L. / Bruner, S.D. | ||||||
![]() | ![]() Title: Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Authors: Li, K. / Condurso, H.L. / Li, G. / Ding, Y. / Bruner, S.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.9 KB | Display | ![]() |
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PDB format | ![]() | 95.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 38026.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 20% PEG 4,000, 20% 2-propanol and 100 mM sodium citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.278→36.027 Å / Num. obs: 28107 / % possible obs: 99 % / Redundancy: 4.9 % / Biso Wilson estimate: 43.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05297 / Net I/σ(I): 17.03 |
Reflection shell | Resolution: 2.278→2.359 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4125 / Mean I/σ(I) obs: 3.56 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.278→36.027 Å
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Refine LS restraints |
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LS refinement shell |
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