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- PDB-8k2n: Crystal structure of Group 4 Monosaccharide-releasing beta-N-acet... -

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Basic information

Entry
Database: PDB / ID: 8k2n
TitleCrystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaLy from Lacticaseibacillus yichunensis, apo form
ComponentsMonosaccharide-releasing beta-N-acetylgalactosaminidase
KeywordsHYDROLASE / Glycoside hydrolase
Biological speciesLacticaseibacillus yichunensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSumida, T. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K05398 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15444 Japan
Mizutani Foundation for GlycoscienceFT100100291 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Authors: Sumida, T. / Hiraoka, S. / Usui, K. / Ishiwata, A. / Sengoku, T. / Stubbs, K.A. / Tanaka, K. / Deguchi, S. / Fushinobu, S. / Nunoura, T.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Monosaccharide-releasing beta-N-acetylgalactosaminidase
C: Monosaccharide-releasing beta-N-acetylgalactosaminidase
A: Monosaccharide-releasing beta-N-acetylgalactosaminidase
B: Monosaccharide-releasing beta-N-acetylgalactosaminidase


Theoretical massNumber of molelcules
Total (without water)244,3354
Polymers244,3354
Non-polymers00
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.930, 94.620, 116.180
Angle α, β, γ (deg.)70.93, 73.81, 72.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Monosaccharide-releasing beta-N-acetylgalactosaminidase


Mass: 61083.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus yichunensis (bacteria)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 4.2, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.01 Å / Num. obs: 107859 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.963 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 5311 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.79 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.883 / SU B: 8.826 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24147 5287 4.9 %RANDOM
Rwork0.18266 ---
obs0.18556 102572 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20.35 Å20.78 Å2
2--1.77 Å20.24 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17040 0 0 514 17554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01117565
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615603
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.64924141
X-RAY DIFFRACTIONr_angle_other_deg0.6891.5536260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85452169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.3785108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04102469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.22709
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0220228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023620
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_it2.982.4658688
X-RAY DIFFRACTIONr_mcbond_other2.982.4658688
X-RAY DIFFRACTIONr_mcangle_it4.373.69310853
X-RAY DIFFRACTIONr_mcangle_other4.373.69310854
X-RAY DIFFRACTIONr_scbond_it3.3442.558877
X-RAY DIFFRACTIONr_scbond_other3.3442.558878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.83.77213289
X-RAY DIFFRACTIONr_long_range_B_refined6.38229.67918366
X-RAY DIFFRACTIONr_long_range_B_other6.3729.67618329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 387 -
Rwork0.24 7590 -
obs--100 %

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