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Yorodumi- PDB-1y7i: Structural and biochemical studies identify tobacco SABP2 as a me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7i | ||||||
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Title | Structural and biochemical studies identify tobacco SABP2 as a methylsalicylate esterase and further implicate it in plant innate immunity, Northeast Structural Genomics Target AR2241 | ||||||
Components | salicylic acid-binding protein 2 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity / systemic acquired resistance, salicylic acid mediated signaling pathway / lipase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / innate immune response Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Forouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. ...Forouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. / Klessig, D.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity Authors: Forouhar, F. / Yang, Y. / Kumar, D. / Chen, Y. / Fridman, E. / Park, S.W. / Chiang, Y. / Acton, T.B. / Montelione, G.T. / Pichersky, E. / Klessig, D.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y7i.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7i.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7i ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7i | HTTPS FTP |
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-Related structure data
Related structure data | 1xklC 1y7hSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Monomer. Although the two monomers in ASU form a dimer, the biochemical data suggest that SABP2 acts as a monomer. |
-Components
#1: Protein | Mass: 30830.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q6RYA0 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 10 mM SA, 0.2 M calcium acetate, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.53 Å / Num. all: 34843 / Num. obs: 34275 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.057 / Net I/σ(I): 15.51 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.47 / Num. unique all: 3227 / Rsym value: 0.261 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y7H Resolution: 2.1→29.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 353462.51 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.8219 Å2 / ksol: 0.327334 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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