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- PDB-8k2j: Crystal structure of Group 3 Oligosaccharide/Monosaccharide-relea... -

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Basic information

Entry
Database: PDB / ID: 8k2j
TitleCrystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm, apo form
ComponentsOligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase
KeywordsHYDROLASE / Glycoside Hydrolase
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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

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Assembly

Deposited unit
A: Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5504
Polymers62,2621
Non-polymers2883
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.379, 53.379, 427.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-970-

HOH

21A-1095-

HOH

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Components

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


Mass: 62261.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 6.0, 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: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→47.8 Å / Num. obs: 64770 / % possible obs: 100 % / Redundancy: 23 % / CC1/2: 0.997 / Net I/σ(I): 10.6
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 3512 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→47.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.314 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21268 3242 5.1 %RANDOM
Rwork0.17996 ---
obs0.18162 59829 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.76→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 15 401 4718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124429
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163998
X-RAY DIFFRACTIONr_angle_refined_deg1.9661.6536024
X-RAY DIFFRACTIONr_angle_other_deg0.6961.5629315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.119542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11810734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
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_it2.5672.2352113
X-RAY DIFFRACTIONr_mcbond_other2.5652.2352113
X-RAY DIFFRACTIONr_mcangle_it3.3963.3342636
X-RAY DIFFRACTIONr_mcangle_other3.3963.3352637
X-RAY DIFFRACTIONr_scbond_it4.3622.6722316
X-RAY DIFFRACTIONr_scbond_other4.2942.6572305
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.13.7963371
X-RAY DIFFRACTIONr_long_range_B_refined7.29429.0814794
X-RAY DIFFRACTIONr_long_range_B_other7.21827.4674716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.803 Å
RfactorNum. reflection% reflection
Rfree1.038 212 -
Rwork1.273 3737 -
obs--85.77 %

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