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- PDB-8ic6: exo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactan... -

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Basic information

Entry
Database: PDB / ID: 8ic6
Titleexo-beta-D-arabinanase ExoMA2 from Microbacterium arabinogalactanolyticum in complex with Tris
Componentsexo-beta-D-arabinanase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homologyMALONATE ION
Function and homology information
Biological speciesMicrobacterium arabinogalactanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFukushima, R. / Kashima, T. / Ishiwata, A. / Fujita, K. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
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 10, 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
B: exo-beta-D-arabinanase
A: exo-beta-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,59325
Polymers190,3742
Non-polymers1,21923
Water29,9231661
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-153 kcal/mol
Surface area53100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.552, 97.511, 139.978
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein exo-beta-D-arabinanase


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 / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1661 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.17386 8854 5 %RANDOM
Rwork0.13757 ---
obs0.13941 167894 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.794 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å21.54 Å2
2---1.11 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: 1 / Resolution: 1.75→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13230 0 71 1661 14962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01213721
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612422
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.64918676
X-RAY DIFFRACTIONr_angle_other_deg1.3271.57628444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38951718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5955149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.668101965
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.21968
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0216819
X-RAY DIFFRACTIONr_gen_planes_other0.0290.023426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1692.0556844
X-RAY DIFFRACTIONr_mcbond_other2.1692.0556842
X-RAY DIFFRACTIONr_mcangle_it2.783.6838552
X-RAY DIFFRACTIONr_mcangle_other2.783.6848553
X-RAY DIFFRACTIONr_scbond_it3.1882.2796877
X-RAY DIFFRACTIONr_scbond_other3.1882.2796878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3554.06510119
X-RAY DIFFRACTIONr_long_range_B_refined5.35221.5816445
X-RAY DIFFRACTIONr_long_range_B_other5.35121.5816446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 668 -
Rwork0.21 12379 -
obs--99.95 %

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