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- PDB-8gjp: A1 Int graft: Adenylation domain 1 core construct from teicoplani... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gjp | |||||||||
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Title | A1 Int graft: Adenylation domain 1 core construct from teicoplanin biosynthesis, intermediate selection pocket graft | |||||||||
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![]() | LIGASE / AMP-binding enzyme / NRPS / Adenylation domain | |||||||||
Function / homology | ![]() siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hansen, M.H. / Cryle, M.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides. Authors: Hansen, M.H. / Adamek, M. / Iftime, D. / Petras, D. / Schuseil, F. / Grond, S. / Stegmann, E. / Cryle, M.J. / Ziemert, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331 KB | Display | ![]() |
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PDB format | ![]() | 263.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 41.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gicSC ![]() 8gj4C ![]() 8gkmC ![]() 8glcC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 42095.703 Da / Num. of mol.: 2 / Mutation: H237Y, L295V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tcp9 / Production host: ![]() ![]() #2: Protein | Mass: 7636.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: tcp13 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 2.696→43.95 Å / Num. obs: 26545 / % possible obs: 99.46 % / Redundancy: 2 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.08666 / Rpim(I) all: 0.08666 / Net I/σ(I): 5.86 |
Reflection shell | Resolution: 2.696→2.792 Å / Rmerge(I) obs: 0.7534 / Num. unique obs: 2529 / CC1/2: 0.499 / Rpim(I) all: 0.7534 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8GIC Resolution: 2.7→43.95 Å / SU ML: 0.3565 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2046 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→43.95 Å
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Refine LS restraints |
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LS refinement shell |
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