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Open data
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Basic information
Entry | Database: PDB / ID: 2zgr | ||||||
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Title | Crystal structure of AAL mutant L33A in C2 spacegroup | ||||||
![]() | Anti-tumor lectin | ||||||
![]() | HYDROLASE / galectin / jelly roll / Apoptosis / Nuclease | ||||||
Function / homology | ![]() DNA nuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / polysaccharide binding / positive regulation of apoptotic process / apoptotic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, N. / Li, D.F. / Wang, D.C. | ||||||
![]() | ![]() Title: Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita Authors: Yang, N. / Li, D.F. / Feng, L. / Xiang, Y. / Liu, W. / Sun, H. / Wang, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.8 KB | Display | ![]() |
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PDB format | ![]() | 30.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zgkC ![]() 2zglSC ![]() 2zgmC ![]() 2zgnC ![]() 2zgoC ![]() 2zgpC ![]() 2zgqC ![]() 2zgsC ![]() 2zgtC ![]() 2zguC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18138.070 Da / Num. of mol.: 1 / Mutation: L33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6WY08, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters |
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#2: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE IS ALLELE OF UNP Q6WY08. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 2M Ammonium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.64 Å / Num. all: 13022 / Num. obs: 13022 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.03 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1895 / Rsym value: 0.175 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZGL Resolution: 1.9→24.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 833685.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.0837 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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