+Open data
-Basic information
Entry | Database: PDB / ID: 2zgp | ||||||
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Title | Crystal structure of Agrocybe aegerita lectin AAL mutant I25G | ||||||
Components | Anti-tumor lectin | ||||||
Keywords | HYDROLASE / galectin / jelly role / Apoptosis / Nuclease | ||||||
Function / homology | Function and homology information 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 | Agrocybe aegerita (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Yang, N. / Li, D.F. / Wang, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zgp.cif.gz | 72.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zgp.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zgp_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 2zgp_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | 2zgp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2zgp_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zgp ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zgp | HTTPS FTP |
-Related structure data
Related structure data | 2zgkC 2zglSC 2zgmC 2zgnC 2zgoC 2zgqC 2zgrC 2zgsC 2zgtC 2zguC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18124.045 Da / Num. of mol.: 2 / Mutation: I25G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe aegerita (fungus) / Gene: AAL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→31.98 Å / Num. all: 10538 / Num. obs: 10538 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.071 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1546 / Rsym value: 0.197 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZGL Resolution: 2.7→31.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 780838.11 / 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: 20.3066 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→31.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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