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- PDB-8ic1: endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium ... -

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Basic information

Entry
Database: PDB / ID: 8ic1
Titleendo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides
Componentsendo-alpha-D-arabinanase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homologyChem-OYO / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMicrobacterium arabinogalactanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLi, J. / Nakashima, C. / 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
A: endo-alpha-D-arabinanase
B: endo-alpha-D-arabinanase
C: endo-alpha-D-arabinanase
D: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,46547
Polymers214,9214
Non-polymers6,54343
Water23,6721314
1
A: endo-alpha-D-arabinanase
B: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,84524
Polymers107,4612
Non-polymers3,38422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-13 kcal/mol
Surface area33660 Å2
MethodPISA
2
C: endo-alpha-D-arabinanase
D: endo-alpha-D-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62023
Polymers107,4612
Non-polymers3,15921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-19 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.708, 137.731, 148.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
endo-alpha-D-arabinanase


Mass: 53730.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium arabinogalactanolyticum (bacteria)
Gene: MIAR_33230 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RIL (DE3)

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Sugars , 2 types, 6 molecules

#2: Polysaccharide alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D- ...alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DArafa1-5DArafa1-5DArafa1-5DArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a122h-1a_1-4]/1-1-1-1/a5-b1_b5-c1_c5-d1WURCSPDB2Glycan 1.1.0
[][a-D-Araf]{[(5+1)][a-D-Araf]{[(5+1)][a-D-Araf]{[(5+1)][a-D-Araf]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose-(1-5)-alpha-D-arabinofuranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DArafa1-5DArafa1-5DArafa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a122h-1a_1-4]/1-1-1/a5-b1_b5-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Araf]{[(5+1)][a-D-Araf]{[(5+1)][a-D-Araf]{}}}LINUCSPDB-CARE

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Non-polymers , 8 types, 1351 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-OYO / (3~{a}~{S},5~{R},6~{R},6~{a}~{S})-5-(hydroxymethyl)-2,2-dimethyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]dioxol-6-ol


Mass: 190.194 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M MES-NaOH (pH 6.0), 5% PEG3000, 20% PEG200, 5 mM arabinononaose with acetonide tag

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2021
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: 1.8→46.65 Å / Num. obs: 217228 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.21 Å2 / CC1/2: 0.625 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 2 / Num. unique obs: 10677 / CC1/2: 0.625 / Rpim(I) all: 0.528

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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: SAD / Resolution: 1.8→46.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.319 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19049 10991 5.1 %RANDOM
Rwork0.15917 ---
obs0.16074 206113 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.52 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14836 0 424 1314 16574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01115729
X-RAY DIFFRACTIONr_bond_other_d0.0030.01614041
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.64621381
X-RAY DIFFRACTIONr_angle_other_deg0.5661.57632290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35351926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.7435105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03102230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.22253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218552
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023872
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_it1.9942.1877674
X-RAY DIFFRACTIONr_mcbond_other1.9942.1877674
X-RAY DIFFRACTIONr_mcangle_it2.523.9229589
X-RAY DIFFRACTIONr_mcangle_other2.523.9229590
X-RAY DIFFRACTIONr_scbond_it2.9352.4768055
X-RAY DIFFRACTIONr_scbond_other2.9352.4768056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2934.411786
X-RAY DIFFRACTIONr_long_range_B_refined5.35623.1718085
X-RAY DIFFRACTIONr_long_range_B_other5.35723.1718086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 737 -
Rwork0.236 15153 -
obs--99.91 %

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