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Yorodumi- PDB-3h2h: Crystal structure of G231F mutant of the rice cell wall degrading... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h2h | ||||||
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Title | Crystal structure of G231F mutant of the rice cell wall degrading esterase LipA from Xanthomonas oryzae | ||||||
Components | esterase | ||||||
Keywords | HYDROLASE / Xanthomonas oryzae pv. oryzae / esterase / cell wall degrading enzyme / rice / virulence / innate immune responses / pathogenesis / glycoside binding | ||||||
Function / homology | Function and homology information triglyceride lipase activity / lipid catabolic process / aminopeptidase activity Similarity search - Function | ||||||
Biological species | Xanthomonas oryzae pv. oryzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Aparna, G. / Chatterjee, A. / Sonti, R.V. / Sankaranarayanan, R. | ||||||
Citation | Journal: Plant Cell / Year: 2009 Title: A Cell Wall-Degrading Esterase of Xanthomonas oryzae Requires a Unique Substrate Recognition Module for Pathogenesis on Rice Authors: Aparna, G. / Chatterjee, A. / Sonti, R.V. / Sankaranarayanan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h2h.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h2h.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/3h2h ftp://data.pdbj.org/pub/pdb/validation_reports/h2/3h2h | HTTPS FTP |
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-Related structure data
Related structure data | 3h2gSC 3h2iC 3h2jC 3h2kC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 42752.762 Da / Num. of mol.: 1 / Fragment: residues in UNP 45-441 / Mutation: G275F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria) Strain: BXO43 / Gene: LipA / Plasmid: pHM1 / Production host: Xanthomonas oryzae pv. oryzae (bacteria) / Strain (production host): BXO43 References: UniProt: Q5H5J0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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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: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 12% PEG 6000, 0.10M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 21553 / Biso Wilson estimate: 16.2 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H2G Resolution: 2.1→24.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1771400.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.1142 Å2 / ksol: 0.339353 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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