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- PDB-6lov: crystal structure of alpha-momorcharin in complex with xanthosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lov | ||||||
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Title | crystal structure of alpha-momorcharin in complex with xanthosine | ||||||
![]() | Ribosome-inactivating protein momordin I | ||||||
![]() | PLANT PROTEIN / alpha-momorcharin / ribosome-inactivating protein / rRNA N-glycosidase / xanthosine | ||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, X. / Jin, T. | ||||||
![]() | ![]() Title: Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs. Authors: Fan, X. / Wang, Y. / Guo, F. / Zhang, Y. / Jin, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 865.2 KB | Display | ![]() |
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Full document | ![]() | 868.5 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6loqC ![]() 6lorC ![]() 6lowC ![]() 6loyC ![]() 6lozC ![]() 6lp0C ![]() 1f8qS 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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Unit cell |
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Components
#1: Protein | Mass: 31562.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-4UO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.349→50 Å / Num. obs: 52296 / % possible obs: 94.1 % / Redundancy: 3.2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5551 / CC1/2: 0.658 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F8Q Resolution: 1.35→18.847 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.384 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.075 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.356 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→18.847 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -20.4273 Å / Origin y: -12.5027 Å / Origin z: -13.3037 Å
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Refinement TLS group | Selection: ALL |