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- PDB-8k2h: Crystal structure of Group 2Oligosaccharide/Monosaccharide-releas... -

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Basic information

Entry
Database: PDB / ID: 8k2h
TitleCrystal structure of Group 2Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GalNAc-thiazoline
ComponentsOligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
KeywordsHYDROLASE / Glycoside hydrolase
Function / homologyGlycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / Chem-GNL / DI(HYDROXYETHYL)ETHER / Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
B: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
A: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9927
Polymers145,3062
Non-polymers6865
Water5,026279
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)68.852, 134.036, 149.969
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 Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase / At1g45150 / Uncharacterized protein At1g45150


Mass: 72653.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g45150, F27F5.22, F27F5_22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y231
#2: Chemical ChemComp-GNL / (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Hepes-Na pH 7.5, 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 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.07 Å / Num. obs: 71289 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.997 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.25 Å / Num. unique obs: 4507 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.967 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22947 3690 5.2 %RANDOM
Rwork0.16892 ---
obs0.17206 67508 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: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å2-0 Å2-0 Å2
2---2.87 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8941 0 43 279 9263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0129269
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168291
X-RAY DIFFRACTIONr_angle_refined_deg2.111.65212658
X-RAY DIFFRACTIONr_angle_other_deg0.6861.55319375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.96451123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.81570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.927101464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.21363
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021857
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_it5.5584.3794492
X-RAY DIFFRACTIONr_mcbond_other5.5584.384492
X-RAY DIFFRACTIONr_mcangle_it7.1796.5485609
X-RAY DIFFRACTIONr_mcangle_other7.186.5495610
X-RAY DIFFRACTIONr_scbond_it6.5514.8144777
X-RAY DIFFRACTIONr_scbond_other6.554.8154778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6137.0047048
X-RAY DIFFRACTIONr_long_range_B_refined10.27556.5999714
X-RAY DIFFRACTIONr_long_range_B_other10.28656.6079682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 274 -
Rwork0.271 4920 -
obs--99.98 %

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