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- PDB-6e58: Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 6.0E+58
TitleCrystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2)
ComponentsSecreted Endo-beta-N-acetylglucosaminidase (EndoS)
KeywordsHYDROLASE / glycoside hydrolase / endo-beta-N-acetylglucosaminidase S2 / endoglycosidase S2 / EndoS2
Function / homologyGlycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / hydrolase activity, hydrolyzing O-glycosyl compounds / Leucine-rich repeat domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / carbohydrate metabolic process / Secreted Endo-beta-N-acetylglucosaminidase (EndoS)
Function and homology information
Biological speciesStreptococcus pyogenes M49 591 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKlontz, E.H. / Trastoy, B. / Gunther, S. / 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
DepositionJul 19, 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Secreted Endo-beta-N-acetylglucosaminidase (EndoS)
B: Secreted Endo-beta-N-acetylglucosaminidase (EndoS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,8454
Polymers181,7652
Non-polymers802
Water5,044280
1
A: Secreted Endo-beta-N-acetylglucosaminidase (EndoS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9222
Polymers90,8821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Secreted Endo-beta-N-acetylglucosaminidase (EndoS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9222
Polymers90,8821
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.169, 105.829, 259.275
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 (resseq 46:47 or resseq 49:142 or (resid...
21(chain B and (resseq 46:47 or resseq 49:56 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASP(chain A and (resseq 46:47 or resseq 49:142 or (resid...AA46 - 474 - 5
12GLNGLNASNASN(chain A and (resseq 46:47 or resseq 49:142 or (resid...AA49 - 1427 - 100
13GLUGLUGLUGLU(chain A and (resseq 46:47 or resseq 49:142 or (resid...AA143101
21THRTHRASPASP(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB46 - 474 - 5
22GLNGLNGLNGLN(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB49 - 567 - 14
23GLUGLUGLUGLU(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB5715
24THRTHRARGARG(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB46 - 8324 - 790
25THRTHRARGARG(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB46 - 8324 - 790
26THRTHRARGARG(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB46 - 8324 - 790
27THRTHRARGARG(chain B and (resseq 46:47 or resseq 49:56 or (resid...BB46 - 8324 - 790

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Components

#1: Protein Secreted Endo-beta-N-acetylglucosaminidase (EndoS)


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 M49 591 (bacteria)
Gene: endoS, Spy49_1414c / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3C1U3
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.37 Å3/Da / Density % sol: 63.45 % / Description: Thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 250 nL 7 mg/mL wild-type EndoS2 + 250 nL mother liquor (0.2 M sodium citrate tribasic, 0.1 M sodium citrate, pH 4, 20% w/v PEG3350) in sitting drops, followed by streak seeding into hanging ...Details: 250 nL 7 mg/mL wild-type EndoS2 + 250 nL mother liquor (0.2 M sodium citrate tribasic, 0.1 M sodium citrate, pH 4, 20% w/v PEG3350) in sitting drops, followed by streak seeding into hanging drops (1 mL 6.6 mg/mL protein + 1 mL mother liquor, single plate-like crystals after three days)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.75→38.89 Å / Num. obs: 60381 / % possible obs: 93.9 % / Redundancy: 3.2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.108 / Rrim(I) all: 0.204 / Net I/σ(I): 6.1 / Num. measured all: 193715 / Scaling rejects: 183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.8230.85343020.3630.5691.03395.7
12.6-38.893.20.0576740.9930.0350.06889.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NUY

4nuy


Resolution: 2.75→38.887 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.264 3042 5.05 %
Rwork0.2093 --
obs0.2121 60280 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.46 Å2 / Biso mean: 38.1406 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: final / Resolution: 2.75→38.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12349 0 2 280 12631
Biso mean--72 34.41 -
Num. residues----1573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912584
X-RAY DIFFRACTIONf_angle_d1.10417038
X-RAY DIFFRACTIONf_chiral_restr0.0611883
X-RAY DIFFRACTIONf_plane_restr0.0072230
X-RAY DIFFRACTIONf_dihedral_angle_d14.8797518
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7151X-RAY DIFFRACTION8.467TORSIONAL
12B7151X-RAY DIFFRACTION8.467TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-2.7930.35131350.30972672280795
2.793-2.83880.39451370.30432545268294
2.8388-2.88770.33221410.29632707284897
2.8877-2.94020.33111520.29032687283998
2.9402-2.99680.32271300.2652667279798
2.9968-3.05790.3691370.26042694283197
3.0579-3.12440.32331560.26042653280997
3.1244-3.1970.29391530.25982661281497
3.197-3.27690.34731380.25792635277395
3.2769-3.36550.26421440.23552542268693
3.3655-3.46450.28781370.24532558269592
3.4645-3.57620.33051290.22052509263890
3.5762-3.70390.28771210.21982347246884
3.7039-3.85210.26391230.20532484260789
3.8521-4.02730.27671320.20522521265390
4.0273-4.23930.24231190.17432590270992
4.2393-4.50460.2221250.16142658278395
4.5046-4.85180.22071440.15272591273593
4.8518-5.33890.20971390.16272538267789
5.3389-6.10890.19141310.17222557268890
6.1089-7.68680.20921670.17842697286494
7.6868-38.89070.18941520.16582725287791

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