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Open data
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Basic information
Entry | Database: PDB / ID: 2zgl | ||||||
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Title | Crystal structure of recombinant Agrocybe aegerita (rAAL) | ||||||
![]() | 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 | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 448.5 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zgkSC ![]() 2zgmC ![]() 2zgnC ![]() 2zgoC ![]() 2zgpC ![]() 2zgqC ![]() 2zgrC ![]() 2zgsC ![]() 2zgtC ![]() 2zguC 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: 18180.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6WY08, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS ALLELE OF UNP Q6WY08. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 50mM Sodium Acetate, 5% PEG 1000, 5% PEG 8000, pH 4.6, 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: Apr 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.66 Å / Num. all: 31292 / Num. obs: 31292 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.9 / Num. unique all: 4557 / Rsym value: 0.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZGK Resolution: 1.9→24.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1001699.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5994 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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