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- PDB-7dfq: Crystal Structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dfq | ||||||
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Title | Crystal Structure of a novel 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase from Fusarium oxysporum 12S, ligand-free form | ||||||
![]() | 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase | ||||||
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Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kondo, T. / Arakawa, T. / Fushinobu, S. / Sakamoto, T. | ||||||
![]() | ![]() Title: Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum. Authors: Kondo, T. / Kichijo, M. / Nakaya, M. / Takenaka, S. / Arakawa, T. / Kotake, T. / Fushinobu, S. / Sakamoto, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 50763.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Sugar | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | Sequence details | The amino acid sequence of 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase (FoBGlcA) has been registered ...The amino acid sequence of 4-O-alpha-L-rhamnosyl-beta-D-glucuronidase (FoBGlcA) has been registered in GenBank, DDBj and EMBL. Its accession number is "LC534636". | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.58 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M MES-NaOH pH6.0, 30% (v/v) PEG mme 2000, 0.1M L-Rha, crystal was soaked into 20% glycerol at 298K for 1 min |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.51→65.86 Å / Num. obs: 68990 / % possible obs: 99.9 % / Redundancy: 6.47 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 39.4 |
Reflection shell | Resolution: 1.51→1.54 Å / Rmerge(I) obs: 0.575 / Num. unique obs: 3158 / CC1/2: 0.891 |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.99 Å2 / Biso mean: 20.313 Å2 / Biso min: 12.19 Å2
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Refinement step | Cycle: final / Resolution: 1.51→42.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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