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- PDB-8ic8: Exo-alpha-D-arabinofuranosidase from Microbacterium arabinogalact... -

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Basic information

Entry
Database: PDB / ID: 8ic8
TitleExo-alpha-D-arabinofuranosidase from Microbacterium arabinogalactanolyticum
ComponentsExo-alpha-D-arabinofuranosidase
KeywordsHYDROLASE / Glycoside hydrolase family 172
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesMicrobacterium arabinogalactanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKashima, T. / Arakawa, T. / Yamada, C. / Ishiwata, A. / Fujita, K. / Fushinobu, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H00929 Japan
Japan Society for the Promotion of Science (JSPS)15H02443 Japan
Japan Society for the Promotion of Science (JSPS)26660083 Japan
Japan Society for the Promotion of Science (JSPS)24380053 Japan
CitationJournal: 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
DepositionFeb 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-alpha-D-arabinofuranosidase
B: Exo-alpha-D-arabinofuranosidase
C: Exo-alpha-D-arabinofuranosidase
D: Exo-alpha-D-arabinofuranosidase
E: Exo-alpha-D-arabinofuranosidase
F: Exo-alpha-D-arabinofuranosidase
G: Exo-alpha-D-arabinofuranosidase
H: Exo-alpha-D-arabinofuranosidase
I: Exo-alpha-D-arabinofuranosidase
J: Exo-alpha-D-arabinofuranosidase
K: Exo-alpha-D-arabinofuranosidase
L: Exo-alpha-D-arabinofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)506,76624
Polymers505,62612
Non-polymers1,14012
Water18,5011027
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90890 Å2
ΔGint-463 kcal/mol
Surface area121970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.109, 207.538, 253.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Exo-alpha-D-arabinofuranosidase


Mass: 42135.508 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium arabinogalactanolyticum (bacteria)
Strain: JCM9171 / Gene: BGN97_09235 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M phosphate citrate, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 26, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→48.24 Å / Num. obs: 264416 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.93 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.057 / Rrim(I) all: 0.158 / Χ2: 0.92 / Net I/σ(I): 9.9
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12946 / CC1/2: 0.85 / Rpim(I) all: 0.239 / Rrim(I) all: 0.661 / Χ2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
BUCCANEERmodel building
REFMAC5.8.0352refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→48.24 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2213 13205 5 %
Rwork0.19 --
obs0.1915 264273 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34813 0 60 1027 35900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00736013
X-RAY DIFFRACTIONf_angle_d0.93949219
X-RAY DIFFRACTIONf_dihedral_angle_d11.3594866
X-RAY DIFFRACTIONf_chiral_restr0.0584991
X-RAY DIFFRACTIONf_plane_restr0.0066511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.440.29524360.23548274X-RAY DIFFRACTION100
2.44-2.470.25534220.22398342X-RAY DIFFRACTION100
2.47-2.50.27514050.22728292X-RAY DIFFRACTION100
2.5-2.530.27274560.2258292X-RAY DIFFRACTION100
2.53-2.570.2674510.2198283X-RAY DIFFRACTION100
2.57-2.60.25344390.21428265X-RAY DIFFRACTION100
2.6-2.640.24814280.20668339X-RAY DIFFRACTION100
2.64-2.680.27744490.21738328X-RAY DIFFRACTION100
2.68-2.720.29014260.22158288X-RAY DIFFRACTION100
2.72-2.760.25614530.21368295X-RAY DIFFRACTION100
2.76-2.810.27854550.22158297X-RAY DIFFRACTION100
2.81-2.860.2784550.22238315X-RAY DIFFRACTION100
2.86-2.920.25174380.21538359X-RAY DIFFRACTION100
2.92-2.980.2544400.22348281X-RAY DIFFRACTION100
2.98-3.040.28134250.22888379X-RAY DIFFRACTION100
3.04-3.110.26934710.22428270X-RAY DIFFRACTION100
3.11-3.190.25814360.22088328X-RAY DIFFRACTION100
3.19-3.280.25513990.21738429X-RAY DIFFRACTION100
3.28-3.370.23974320.20558325X-RAY DIFFRACTION100
3.37-3.480.21614600.19318339X-RAY DIFFRACTION100
3.48-3.610.21574140.18998391X-RAY DIFFRACTION100
3.61-3.750.21424570.18528367X-RAY DIFFRACTION100
3.75-3.920.19534510.16348370X-RAY DIFFRACTION100
3.92-4.130.16524460.14888372X-RAY DIFFRACTION100
4.13-4.390.1554330.14268457X-RAY DIFFRACTION100
4.39-4.730.15984850.14128368X-RAY DIFFRACTION100
4.73-5.20.16764280.14638473X-RAY DIFFRACTION100
5.2-5.950.19844180.16438536X-RAY DIFFRACTION100
5.95-7.490.19644180.19388585X-RAY DIFFRACTION100
7.5-48.240.20184790.18698829X-RAY DIFFRACTION100

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