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Yorodumi- PDB-3tw5: Crystal structure of the GP42 transglutaminase from Phytophthora sojae -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tw5 | ||||||
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Title | Crystal structure of the GP42 transglutaminase from Phytophthora sojae | ||||||
Components | Transglutaminase elicitor | ||||||
Keywords | TRANSFERASE / Cysteine protease / Convergent evolution / Innate immunity / Pathogen-associated molecular pattern (PAMP) / Phytophthora / tranglutaminase | ||||||
Function / homology | Function and homology information protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity Similarity search - Function | ||||||
Biological species | Phytophthora sojae (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.95 Å | ||||||
Authors | Reiss, K. / Kirchner, E. / Zocher, G. / Stehle, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural and Phylogenetic Analyses of the GP42 Transglutaminase from Phytophthora sojae Reveal an Evolutionary Relationship between Oomycetes and Marine Vibrio Bacteria. Authors: Reiss, K. / Kirchner, E. / Gijzen, M. / Zocher, G. / Loffelhardt, B. / Nurnberger, T. / Stehle, T. / Brunner, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tw5.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tw5.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tw5_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 3tw5_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 3tw5_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 3tw5_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/3tw5 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3tw5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 40224.648 Da / Num. of mol.: 2 / Fragment: transglutaminase domain / Mutation: C290S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora sojae (eukaryote) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 References: UniProt: Q6Q475, UniProt: Q01928*PLUS, protein-glutamine gamma-glutamyltransferase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 11 Details: 1.6M ammonium sulfate, 0.2M lithium sulfate, 0.1M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), pH 11.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.95→30 Å / Num. all: 33060 / Num. obs: 31882 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.09 / Net I/σ(I): 15.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.95→3.026 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.75 / Rsym value: 0.583 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.137 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.922 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2604 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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