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Yorodumi- PDB-8ic6: exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ic6 | ||||||||||||
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Title | exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris | ||||||||||||
Components | exo-beta-D-arabinanase | ||||||||||||
Keywords | HYDROLASE / Glycoside Hydrolase | ||||||||||||
Function / homology | MALONATE ION Function and homology information | ||||||||||||
Biological species | Microbacterium arabinogalactanolyticum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||||||||
Authors | Fukushima, R. / Kashima, T. / Ishiwata, A. / Fujita, K. / Fushinobu, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria. Authors: Shimokawa, M. / Ishiwata, A. / Kashima, T. / Nakashima, C. / Li, J. / Fukushima, R. / Sawai, N. / Nakamori, M. / Tanaka, Y. / Kudo, A. / Morikami, S. / Iwanaga, N. / Akai, G. / Shimizu, N. / ...Authors: Shimokawa, M. / Ishiwata, A. / Kashima, T. / Nakashima, C. / Li, J. / Fukushima, R. / Sawai, N. / Nakamori, M. / Tanaka, Y. / Kudo, A. / Morikami, S. / Iwanaga, N. / Akai, G. / Shimizu, N. / Arakawa, T. / Yamada, C. / Kitahara, K. / Tanaka, K. / Ito, Y. / Fushinobu, S. / Fujita, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ic6.cif.gz | 383.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ic6.ent.gz | 300.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ic6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ic6_validation.pdf.gz | 479.6 KB | Display | wwPDB validaton report |
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Full document | 8ic6_full_validation.pdf.gz | 494.7 KB | Display | |
Data in XML | 8ic6_validation.xml.gz | 74.7 KB | Display | |
Data in CIF | 8ic6_validation.cif.gz | 115.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/8ic6 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/8ic6 | HTTPS FTP |
-Related structure data
Related structure data | 8hhvC 8ic1C 8ic7C 8ic8C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 95186.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium arabinogalactanolyticum (bacteria) Gene: MIAR_33170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RIL (DE3) |
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-Non-polymers , 6 types, 1684 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-MLI / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.9 / Details: 0.18 M MgCl2, 0.1 M Tris-HCl (pH 9.0), 14% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2022 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.76 Å / Num. obs: 176777 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.64 Å2 / CC1/2: 0.874 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.043 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 8703 / CC1/2: 0.873 / Rpim(I) all: 0.246 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→48.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.794 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→48.8 Å
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Refine LS restraints |
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