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- PDB-8i4d: X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i4d | ||||||||||||
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Title | X-ray structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex at 100K | ||||||||||||
![]() | L-Rhamnose-alpha-1,4-D-glucuronate lyase | ||||||||||||
![]() | LYASE / polysaccharide lyase / gum arabic / carbohydrate-active enzyme | ||||||||||||
Function / homology | BNR repeat-containing family member / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / ACETATE ION / alpha-L-rhamnopyranose / L-Rhamnose-alpha-1,4-D-glucuronate lyase![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yano, N. / Kondo, T. / Kusaka, K. / Yamada, T. / Arakawa, T. / Sakamoto, T. / Fushinobu, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Charge neutralization and beta-elimination cleavage mechanism of family 42 L-rhamnose-alpha-1,4-D-glucuronate lyase revealed using neutron crystallography. Authors: Yano, N. / Kondo, T. / Kusaka, K. / Arakawa, T. / Sakamoto, T. / Fushinobu, S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yqsSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50085.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/RAM.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-RAM / |
-Non-polymers , 5 types, 462 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / |
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#5: Chemical | ChemComp-TRS / |
#6: Chemical | ChemComp-CA / |
#7: Chemical | ChemComp-NA / |
#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PROTEIN SOLUTION : PROTEIN 24MG/ML, 20MM TRIS-DCL (PD 8.0), RESERVOIR SOLUTION : 36 % (W/V) PEG 1500, 0.1 M TRIS-DCL (PD 8.5), 0.1 M L-RHA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→42.63 Å / Num. obs: 180680 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.06→1.08 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8886 / CC1/2: 0.814 / Rpim(I) all: 0.323 / Rrim(I) all: 1.124 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YQS Resolution: 1.06→41.65 Å / SU ML: 0.088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8128 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→41.65 Å
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Refine LS restraints |
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LS refinement shell |
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