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Open data
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Basic information
Entry | Database: PDB / ID: 8kdl | ||||||
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Title | Crystal structure of LmbF in complex with PLP | ||||||
![]() | Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme | ||||||
![]() | LYASE / lincomycin / PLP / biosynthesis | ||||||
Function / homology | : / biosynthetic process / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / LmbF![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mori, T. / Lyu, S. / Kadlcik, S. / Abe, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure of LmbF in complex with PLP Authors: Mori, T. / Lyu, S. / Kadlcik, S. / Abe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235 KB | Display | ![]() |
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PDB format | ![]() | 148.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48373.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5, 27% PEG 4000, 0.8M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.63 Å / Num. obs: 80638 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 11.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3 / Num. unique obs: 4199 / CC1/2: 0.841 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→48.63 Å
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Refine LS restraints |
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LS refinement shell |
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