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Yorodumi- PDB-1nh1: Crystal Structure of the Type III Effector AvrB from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nh1 | ||||||
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Title | Crystal Structure of the Type III Effector AvrB from Pseudomonas syringae. | ||||||
Components | Avirulence B protein | ||||||
Keywords | Avirulence Protein / HELIX BUNDLE | ||||||
Function / homology | Fic-like fold - #20 / Avirulence B/C / Avirulence B/C superfamily / Avirulence protein / Fic-like fold / Orthogonal Bundle / extracellular region / Mainly Alpha / Avirulence protein B Function and homology information | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Lee, C.C. / Wood, M.D. / Ng, K. / Luginbuhl, P. / Spraggon, G. / Katagiri, F. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Crystal Structure of the Type III Effector AvrB from Pseudomonas syringae. Authors: Lee, C.C. / Wood, M.D. / Ng, K. / Luginbuhl, P. / Spraggon, G. / Katagiri, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nh1.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nh1.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nh1_validation.pdf.gz | 366.4 KB | Display | wwPDB validaton report |
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Full document | 1nh1_full_validation.pdf.gz | 377 KB | Display | |
Data in XML | 1nh1_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1nh1_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nh1 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nh1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37097.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: AVRB / Plasmid: pET-27b(+) / Cell line (production host): BL21 (DE3) pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: P13835 |
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#2: 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: 68.01 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 29594 / Num. obs: 27892 / % possible obs: 94.2 % | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 93.4 % / Rmerge(I) obs: 0.066 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 64.6 % / Rmerge(I) obs: 0.493 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.2→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refinement | *PLUS Lowest resolution: 500 Å / Rfactor Rfree: 0.275 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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