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- PDB-2xhn: Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xhn | |||||||||
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Title | Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant | |||||||||
![]() | RHAMNOGALACTURONASE B | |||||||||
![]() | LYASE / CARBOHYDRATE ACTIVE ENZYME / PECTIN / DEGRADATION / POLYSACCHARIDE LYASE FAMILY 4 | |||||||||
Function / homology | ![]() rhamnogalacturonan endolyase / rhamnogalacturonan endolyase activity / pectin catabolic process / cell wall organization / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jensen, M.H. / Otten, H. / Christensen, U. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. / Lo Leggio, L. | |||||||||
![]() | ![]() Title: Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus Aculeatus. Authors: Jensen, M.H. / Otten, H. / Christensen, U. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. / Leggio, L.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 594.8 KB | Display | ![]() |
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PDB format | ![]() | 494.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.2 KB | Display | ![]() |
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Full document | ![]() | 457.7 KB | Display | |
Data in XML | ![]() | 53.7 KB | Display | |
Data in CIF | ![]() | 88.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3njvC ![]() 3njxC ![]() 1nkgS 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 54185.422 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: 20% PEG 4000, 0.1 AMMONIUM SULFATE, HANGING DROP VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 16, 2006 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL |
Radiation | Monochromator: BENT SI (220) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→20 Å / Num. obs: 142062 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 10.01 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 9.7 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NKG Resolution: 1.52→20.007 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 15.82 / Stereochemistry target values: ML Details: RESIDUES GLN20, ASN435 AND THR493 ARE IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT IN BOTH CHAINS, BUT WELL SUPPORTED BY ELECTRON DENSITY AS IN THE NATIVE PDB 1NKG. THE LEU377 RESIDUE IS ...Details: RESIDUES GLN20, ASN435 AND THR493 ARE IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT IN BOTH CHAINS, BUT WELL SUPPORTED BY ELECTRON DENSITY AS IN THE NATIVE PDB 1NKG. THE LEU377 RESIDUE IS DISORDERED IN BOTH CHAINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.768 Å2 / ksol: 0.409 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.52→20.007 Å
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Refine LS restraints |
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LS refinement shell |
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