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Yorodumi- PDB-2nud: The structure of the type III effector AvrB complexed with a high... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nud | ||||||
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Title | The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide | ||||||
Components |
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Keywords | TOXIN/PROTEIN BINDING / AvrB RIN4 high-affinity crystal structure / TOXIN-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of plant-type hypersensitive response / defense response to bacterium => GO:0042742 / plant-type hypersensitive response / innate immune response-activating signaling pathway / extrinsic component of plasma membrane / endomembrane system / response to molecule of bacterial origin / protein phosphorylation / extracellular region / membrane ...negative regulation of plant-type hypersensitive response / defense response to bacterium => GO:0042742 / plant-type hypersensitive response / innate immune response-activating signaling pathway / extrinsic component of plasma membrane / endomembrane system / response to molecule of bacterial origin / protein phosphorylation / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas syringae pv. glycinea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Singer, A.U. / Desveaux, D. / Wu, A.J. / McNulty, B. / Sondek, J. / Dangl, J.L. | ||||||
Citation | Journal: Plos Pathog. / Year: 2007 Title: Type III Effector Activation via Nucleotide Binding, Phosphorylation, and Host Target Interaction. Authors: Desveaux, D. / Singer, A.U. / Wu, A.J. / McNulty, B.C. / Musselwhite, L. / Nimchuk, Z. / Sondek, J. / Dangl, J.L. | ||||||
History |
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Remark 400 | COMPOUND THE AUTHORS STATE THAT FOR THE PEPTIDE (CHAINS C AND D), THE N- AND C-TERMINI ARE BLOCKED ...COMPOUND THE AUTHORS STATE THAT FOR THE PEPTIDE (CHAINS C AND D), THE N- AND C-TERMINI ARE BLOCKED (ACETYLATED AT THE N-TERMINUS AND AMIDATED AT THE C-TERMINUS). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nud.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nud.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 2nud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nud ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nud | HTTPS FTP |
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-Related structure data
Related structure data | 2nunC 1nh1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | chain B and D (AvrB and peptide complex no 2) are generated from chains A and C (complex no 1) by applying the transformation to complex 1 of: [-1 0.0004 0.0008 + [-0.0584 -0.0004 -1 0.0023 -10.7947 0.0008 0.0023 1 ] -59.8951] (in the form of [x11 x12 x13 + [y1 x21 x22 x23 y2 x31 x32 x33] y3] ) |
-Components
#1: Protein | Mass: 36181.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. glycinea (bacteria) Species: Pseudomonas savastanoi / Strain: pv glycinea / Gene: avrB / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P13835 #2: Protein/peptide | Mass: 4068.417 Da / Num. of mol.: 2 / Fragment: RIN4 peptide, residues 142-176 / Source method: obtained synthetically Details: RIN4 peptide synthesized naturally from the Arabidopsis RIN4 sequence. N- and C-termini blocked by methylation and amidation, respectively References: UniProt: Q8GYN5 #3: Chemical | ChemComp-TRS / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 1.98 Å3/Da / Density % sol: 38.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1:2-3 ratio of protein to peptide with AvrB at ~12 mg/ml mixed with an equal volume of well solution (100 mM Tris, pH 7.5, 20-30% PEG 550 MME), VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2004 / Details: Osmic Confocal "Blue" |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→99 Å / Num. all: 29016 / Num. obs: 29016 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.6 / % possible all: 72.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NH1 Resolution: 2.3→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1203820.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.7896 Å2 / ksol: 0.350678 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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