+Open data
-Basic information
Entry | Database: PDB / ID: 3hgl | ||||||
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Title | crystal of AvrPtoB 121-205 | ||||||
Components | Effector protein hopAB2 | ||||||
Keywords | LIGASE / five helices / Hypersensitive response elicitation / Secreted / Ubl conjugation / Ubl conjugation pathway / Virulence | ||||||
Function / homology | Function and homology information effector-mediated suppression of host pattern-triggered immunity / symbiont-mediated perturbation of host defense-related programmed cell death / Transferases; Acyltransferases; Aminoacyltransferases / transferase activity / extracellular region Similarity search - Function | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Dong, J. / Xiao, F. / Fan, F. / Gu, L. / Cang, H. / Martin, G.B. / Chai, J. | ||||||
Citation | Journal: Plant Cell / Year: 2009 Title: Crystal Structure of the Complex between Pseudomonas Effector AvrPtoB and the Tomato Pto Kinase Reveals Both a Shared and a Unique Interface Compared with AvrPto-Pto Authors: Dong, J. / Xiao, F. / Fan, F. / Gu, L. / Cang, H. / Martin, G.B. / Chai, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hgl.cif.gz | 23.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hgl.ent.gz | 18.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/3hgl ftp://data.pdbj.org/pub/pdb/validation_reports/hg/3hgl | HTTPS FTP |
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-Related 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: 9616.225 Da / Num. of mol.: 1 / Fragment: UNP residues 121-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Gene: hopAB2, avrPtoB, PSPTO_3087 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8RSY1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60% (v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9789, 0.9794, 0.9764 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 7, 2008 | ||||||||||||
Radiation | Monochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→99 Å / Num. all: 12921 / Num. obs: 12921 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 22.4 | ||||||||||||
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.33 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.96 Å / Total num. of bins used: 12
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