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- PDB-7y02: Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-ox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y02 | ||||||
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Title | Crystal structure of Ricin A chain bound with (S)-2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)-3-(4-fluorophenyl)propanoic acid | ||||||
![]() | Ricin A chain | ||||||
![]() | HYDROLASE / HYDROLASE INHIBITOR | ||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Goto, M. / Higashi, S. / Ohba, T. / Kawata, R. / Nagatsu, K. / Suzuki, S. / Saito, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational change in ricin toxin A-Chain: A critical factor for inhibitor binding to the secondary pocket. Authors: Goto, M. / Higashi, S. / Ohba, T. / Kawata, R. / Nagatsu, K. / Suzuki, S. / Anslyn, E.V. / Saito, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973.3 KB | Display | ![]() |
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Full document | ![]() | 974.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xzsC ![]() 7xztC ![]() 7xzuC ![]() 7xzwC ![]() 7y03C ![]() 7y05C ![]() 7y06C ![]() 7y07C ![]() 7y08C ![]() 4huoS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 30896.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 2000, Lithium sulfate, Sodium acetate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→61.038 Å / Num. all: 44255 / Num. obs: 44255 / % possible obs: 100 % / Redundancy: 12.8 % / Rpim(I) all: 0.009 / Rrim(I) all: 0.033 / Rsym value: 0.032 / Net I/av σ(I): 15.9 / Net I/σ(I): 40.9 / Num. measured all: 568453 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HUO Resolution: 1.6→48.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.781 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.86 Å2 / Biso mean: 29.355 Å2 / Biso min: 16.59 Å2
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Refinement step | Cycle: final / Resolution: 1.6→48.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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