+Open data
-Basic information
Entry | Database: PDB / ID: 2nun | ||||||
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Title | The structure of the type III effector AvrB complexed with ADP | ||||||
Components | Avirulence B protein | ||||||
Keywords | TOXIN/PROTEIN BINDING / type III effector / AvrB / nuclotide / pocket / ADP / TOXIN-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas syringae pv. glycinea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Singer, A.U. / Desveaux, D. / Wu, A.J. / McNulty, B. / Dangl, J.L. / Sondek, J. | ||||||
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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nun.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nun.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nun_validation.pdf.gz | 809 KB | Display | wwPDB validaton report |
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Full document | 2nun_full_validation.pdf.gz | 818.5 KB | Display | |
Data in XML | 2nun_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 2nun_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nun ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nun | HTTPS FTP |
-Related structure data
Related structure data | 2nudC 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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Unit cell |
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Details | only one molecule in the asymmetric unit and the biological assembly |
-Components
#1: Protein | Mass: 36181.262 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-TRS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Protein (8-10 mg/ml) was mixed with well solution (100 mM Glycine, pH 9.0, 20-30% PEG 550 MME)at a 1:1 ratio. Microseeding was employed to obtain better crystals. Nucleotides were ...Details: Protein (8-10 mg/ml) was mixed with well solution (100 mM Glycine, pH 9.0, 20-30% PEG 550 MME)at a 1:1 ratio. Microseeding was employed to obtain better crystals. Nucleotides were incorporated by exchanging drop and resevoir solutions with 20 l 27% PEG 500 MME and 100 mM Tris 7.5 plus 5 mM MgCl2, followed by a final exchange of this solution plus 5 mM nucleotide. Nucleotides were soaked for ~ 1 day. , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 29955 / Num. obs: 24091 / % possible obs: 80.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.63 / Num. unique all: 943 / % possible all: 32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NH1 Resolution: 2.4→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1928271.38 / 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: 32.5504 Å2 / ksol: 0.30493 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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