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- PDB-6mds: Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 6mds
TitleCrystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2) with complex biantennary glycan
ComponentsEndo-beta-N-acetylglucosaminidase
KeywordsHYDROLASE / glycoside hydrolase / endo-beta-N-acetylglucosaminidase S2 / endoglycosidase S2 / EndoS2
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / evasion of host immune response / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Leucine-rich repeat domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-beta-N-acetylglucosaminidase EndoS2
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKlontz, E.H. / Trastoy, B. / Orwenyo, J. / Wang, L.X. / Guerin, M.E. / Sundberg, E.J.
CitationJournal: ACS Cent Sci / Year: 2019
Title: Molecular Basis of Broad SpectrumN-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2.
Authors: Klontz, E.H. / Trastoy, B. / Deredge, D. / Fields, J.K. / Li, C. / Orwenyo, J. / Marina, A. / Beadenkopf, R. / Gunther, S. / Flores, J. / Wintrode, P.L. / Wang, L.X. / Guerin, M.E. / Sundberg, E.J.
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase
B: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,7216
Polymers181,7652
Non-polymers2,9574
Water7,566420
1
A: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3613
Polymers90,8821
Non-polymers1,4782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3613
Polymers90,8821
Non-polymers1,4782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.378, 105.514, 259.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 46 and (name O or name...
21(chain B and ((resid 46 and (name N or name...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTHRTHR(chain A and ((resid 46 and (name O or name...AA464
121THRTHRARGARG(chain A and ((resid 46 and (name O or name...AA46 - 8324 - 790
131THRTHRARGARG(chain A and ((resid 46 and (name O or name...AA46 - 8324 - 790
141THRTHRARGARG(chain A and ((resid 46 and (name O or name...AA46 - 8324 - 790
151THRTHRARGARG(chain A and ((resid 46 and (name O or name...AA46 - 8324 - 790
161THRTHRARGARG(chain A and ((resid 46 and (name O or name...AA46 - 8324 - 790
211THRTHRTHRTHR(chain B and ((resid 46 and (name N or name...BB464
221THRTHRARGARG(chain B and ((resid 46 and (name N or name...BB46 - 8324 - 790
231THRTHRARGARG(chain B and ((resid 46 and (name N or name...BB46 - 8324 - 790
241THRTHRARGARG(chain B and ((resid 46 and (name N or name...BB46 - 8324 - 790
251THRTHRARGARG(chain B and ((resid 46 and (name N or name...BB46 - 8324 - 790
261THRTHRARGARG(chain B and ((resid 46 and (name N or name...BB46 - 8324 - 790
112NAGNAGGALGALchain CCC1 - 8
212NAGNAGGALGALchain DDD1 - 8

NCS ensembles :
ID
1
2

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase / EndoS2


Mass: 90882.273 Da / Num. of mol.: 2 / Fragment: UNP residues 44-843
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ndoS2 / Production host: Escherichia coli (E. coli) / References: UniProt: T1WGN1
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1438.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3-1-4-3-1-4/a4-b1_b3-c1_b6-f1_c2-d1_d4-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.43 Å3/Da / Density % sol: 64.14 % / Description: Thin plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M sodium citrate tribasic, 0.1 M sodium citrate, pH 4, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→39.712 Å / Num. obs: 75988 / % possible obs: 90 % / Redundancy: 4.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.08 / Rrim(I) all: 0.174 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.554.11.11546630.4620.5861.26993.7
12.5-39.714.30.0435600.9970.0220.04976.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E58

6e58


Resolution: 2.5→39.712 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.4
RfactorNum. reflection% reflection
Rfree0.2418 3796 5 %
Rwork0.193 --
obs0.1955 75877 88.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.55 Å2 / Biso mean: 48.6985 Å2 / Biso min: 22.4 Å2
Refinement stepCycle: final / Resolution: 2.5→39.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12459 0 198 420 13077
Biso mean--66.38 47.06 -
Num. residues----1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912904
X-RAY DIFFRACTIONf_angle_d1.20417476
X-RAY DIFFRACTIONf_chiral_restr0.0651966
X-RAY DIFFRACTIONf_plane_restr0.0072251
X-RAY DIFFRACTIONf_dihedral_angle_d14.0367751
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7168X-RAY DIFFRACTION7.139TORSIONAL
12B7168X-RAY DIFFRACTION7.139TORSIONAL
21A136X-RAY DIFFRACTION7.139TORSIONAL
22B136X-RAY DIFFRACTION7.139TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.53170.33431320.29862734286692
2.5317-2.5650.36241400.29462806294693
2.565-2.60010.34481430.28992730287392
2.6001-2.63730.37731420.29532769291192
2.6373-2.67660.34741330.28562696282991
2.6766-2.71840.33761560.27562737289392
2.7184-2.7630.34871510.27042701285291
2.763-2.81060.31511420.26812687282990
2.8106-2.86170.35361400.25752736287691
2.8617-2.91680.2971330.2542729286291
2.9168-2.97630.31611600.25692720288091
2.9763-3.0410.33151490.24632694284391
3.041-3.11170.25641540.23022693284790
3.1117-3.18950.32521570.23252701285890
3.1895-3.27570.26161410.21832700284190
3.2757-3.3720.27531550.20922660281589
3.372-3.48080.24791410.21042581272286
3.4808-3.60510.25261440.19652648279288
3.6051-3.74930.20411620.17682635279788
3.7493-3.91980.23541260.16762635276187
3.9198-4.12630.20651320.15132627275987
4.1263-4.38450.17141120.14322664277687
4.3845-4.72250.17071230.13542571269484
4.7225-5.19690.1721340.13762613274785
5.1969-5.94670.19471210.1572602272384
5.9467-7.4840.21511210.16882491261280
7.484-39.7170.16561520.1452521267378

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