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- PDB-3h2j: Crystal structure of the rice cell wall degrading esterase LipA f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h2j | ||||||
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Title | Crystal structure of the rice cell wall degrading esterase LipA from Xanthomonas oryzae | ||||||
![]() | esterase![]() | ||||||
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Function / homology | ![]() ![]() ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.1 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3h2gSC ![]() 3h2hC ![]() 3h2iC ![]() 3h2kC 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, ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 48% PEG 400, 0.10M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.89→25 Å / Num. obs: 27294 / Biso Wilson estimate: 19.9 Å2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3H2G Resolution: 1.89→24.2 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1612603.41 / 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: 59.0006 Å2 / ksol: 0.361392 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.89→24.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.96 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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