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Yorodumi- PDB-1s21: Crystal Structure of AvrPphF ORF2, A Type III Effector from P. sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s21 | ||||||
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Title | Crystal Structure of AvrPphF ORF2, A Type III Effector from P. syringae | ||||||
Components | ORF2 | ||||||
Keywords | CHAPERONE / PREDOMINANTLY BETA-STRAND | ||||||
Function / homology | Type III effector HopF2 / AvrPphF-ORF-2 / ORF2 Function and homology information | ||||||
Biological species | Pseudomonas syringae pv. phaseolicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2 Å | ||||||
Authors | Singer, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.K. / Sondek, J. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structures of the Type III Effector Protein AvrPphF and Its Chaperone Reveal Residues Required for Plant Pathogenesis Authors: Singer, A.U. / Desveaux, D. / Betts, L. / Chang, J.H. / Nimchuk, Z. / Grant, S.R. / Dangl, J.K. / Sondek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s21.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s21.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s21_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 1s21_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 1s21_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1s21_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/1s21 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/1s21 | HTTPS FTP |
-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: 22050.238 Da / Num. of mol.: 1 / Fragment: AvrPphF ORF2 / Mutation: none Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola (bacteria) Species: Pseudomonas savastanoi / Gene: AvrPphF ORF2 / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL Codon Plus / References: UniProt: Q9K2L5 |
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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 |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||
Detector |
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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→50 Å / Num. all: 16474 / Num. obs: 16442 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.9 | |||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1601 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2→19.63 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1137637.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1586 Å2 / ksol: 0.358902 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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