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Yorodumi- PDB-6s2p: Structure of the NB-ARC domain from the Tomato immune receptor NRC1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s2p | ||||||
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Title | Structure of the NB-ARC domain from the Tomato immune receptor NRC1 | ||||||
Components | NRC1 | ||||||
Keywords | PLANT PROTEIN / NLR receptor / NB-ARC domain / plant immunity | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Steele, J.F.C. / Banfield, M.J. | ||||||
Citation | Journal: Plos One / Year: 2019 Title: Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor. Authors: Steele, J.F.C. / Hughes, R.K. / Banfield, M.J. #1: Journal: Biorxiv / Year: 2019 Title: Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor Authors: Steele, J.F.C. / Hughes, R.K. / Banfield, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s2p.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s2p.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s2p_validation.pdf.gz | 791.4 KB | Display | wwPDB validaton report |
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Full document | 6s2p_full_validation.pdf.gz | 795.3 KB | Display | |
Data in XML | 6s2p_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 6s2p_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/6s2p ftp://data.pdbj.org/pub/pdb/validation_reports/s2/6s2p | 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: 40151.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: A1X877, UniProt: A0A3Q7EK40*PLUS |
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#2: Chemical | ChemComp-ADP / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 8% PEG 1500, 0.1 M MMT (MES, malic acid and Tris,) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 13066 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1463 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→47.855 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0.62 / Phase error: 42.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.59 Å2 / Biso mean: 83.3549 Å2 / Biso min: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.855 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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