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Yorodumi- PDB-8ic7: exo-beta-D-arabinofuranosidase ExoMA2 from Microbacterium arabino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ic7 | ||||||||||||
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Title | exo-beta-D-arabinofuranosidase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with beta-D-arabinofuranose | ||||||||||||
Components | exo-beta-D-arabinofuranosidase | ||||||||||||
Keywords | HYDROLASE / Glycoside Hydrolase | ||||||||||||
Function / homology | beta-D-arabinofuranose Function and homology information | ||||||||||||
Biological species | Microbacterium arabinogalactanolyticum (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 8ic7.cif.gz | 383.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ic7.ent.gz | 300.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ic7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ic7_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8ic7_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8ic7_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 8ic7_validation.cif.gz | 114.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/8ic7 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/8ic7 | HTTPS FTP |
-Related structure data
Related structure data | 8hhvC 8ic1C 8ic6C 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 / Sugars , 2 types, 7 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) #4: Sugar | ChemComp-BXX / |
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-Non-polymers , 4 types, 1650 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: 0.2 M MgCl2, 0.1 M CHES-NaOH (pH 8.9), 14% PEG8000, 100 mM D-arabinose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 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: 1.35→48.62 Å / Num. obs: 382283 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.28 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1 / Num. unique obs: 18879 / CC1/2: 0.609 / Rpim(I) all: 0.629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→45.87 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.051 / 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: 17.61 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→45.87 Å
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Refine LS restraints |
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