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- PDB-3h2k: Crystal structure of a ligand-bound form of the rice cell wall de... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h2k | ||||||
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Title | Crystal structure of a ligand-bound form of the rice cell wall degrading esterase LipA from Xanthomonas oryzae | ||||||
![]() | esterase | ||||||
![]() | HYDROLASE / Xanthomonas oryzae pv. oryzae / esterase / cell wall degrading enzyme / rice / virulence / innate immune responses / pathogenesis / glycoside binding | ||||||
Function / homology | ![]() triacylglycerol lipase activity / aminopeptidase activity / lipid catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Aparna, G. / Chatterjee, A. / Sonti, R.V. / Sankaranarayanan, R. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 825 KB | Display | ![]() |
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Full document | ![]() | 830.5 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h2gSC ![]() 3h2hC ![]() 3h2iC ![]() 3h2jC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42662.637 Da / Num. of mol.: 1 / Fragment: residues in UNP 45-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: BXO43 / Gene: LipA / Plasmid: pHM1 / Production host: ![]() References: UniProt: Q5H5J0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 Details: 12% PEG 6000, 0.10M MES, 17.5mM BOG, pH 6.7, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2007 |
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: 23753 / Biso Wilson estimate: 25.4 Å2 |
Reflection shell | Resolution: 2.1→2.18 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H2G Resolution: 2.1→24.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1641582.14 / 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: 50.1022 Å2 / ksol: 0.347913 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file |
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