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- PDB-8a49: Endoglycosidase S in complex with IgG1 Fc -

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Basic information

Entry
Database: PDB / ID: 8a49
TitleEndoglycosidase S in complex with IgG1 Fc
Components
  • IgG1 Fc
  • Secreted endoglycosidase EndoS
KeywordsIMMUNE SYSTEM / Endoglycosidase / antibody / complex
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 / Glycoside hydrolase superfamily / carbohydrate metabolic process / Secreted endoglycosidase EndoS
Function and homology information
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsSudol, A.S.L. / Tews, I. / Crispin, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2022
Title: Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS.
Authors: Sudol, A.S.L. / Butler, J. / Ivory, D.P. / Tews, I. / Crispin, M.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: 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
Revision 1.2Jan 11, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG1 Fc
C: Secreted endoglycosidase EndoS
D: Secreted endoglycosidase EndoS
B: IgG1 Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,4905
Polymers256,0274
Non-polymers1,4631
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint7 kcal/mol
Surface area97130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.529, 174.294, 193.059
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
11A
21A
32A
42A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A238 - 444
2111A238 - 444
3221A103 - 990
4221A103 - 990

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Antibody IgG1 Fc


Mass: 25641.098 Da / Num. of mol.: 2 / Mutation: E382R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSE-hIgG1-Fc / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
#2: Protein Secreted endoglycosidase EndoS


Mass: 102372.328 Da / Num. of mol.: 2 / Mutation: D233A, E235L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ndoS / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9APG4
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-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][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M buffer system 2 (Sodium HEPES; MOPS (acid)), pH 7.5, 37.5 % v/v precipitant mix 4 (25% v/v MPD; 25% PEG ...Details: 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M buffer system 2 (Sodium HEPES; MOPS (acid)), pH 7.5, 37.5 % v/v precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) - condition B8 from Morpheus crystallisation screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→49.78 Å / Num. obs: 43678 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.04 / Rrim(I) all: 0.15 / Net I/σ(I): 11.2
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.951 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2124 / CC1/2: 0.599 / Rpim(I) all: 0.532 / Rrim(I) all: 2.023 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EN3

6en3


Resolution: 3.45→49.78 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.747 / SU B: 55.56 / SU ML: 0.758 / Cross valid method: FREE R-VALUE / ESU R Free: 0.701
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3112 2116 4.852 %
Rwork0.2525 41497 -
all0.255 --
obs-43613 99.954 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 146.604 Å2
Baniso -1Baniso -2Baniso -3
1-2.654 Å2-0 Å20 Å2
2--2.667 Å2-0 Å2
3----5.322 Å2
Refinement stepCycle: LAST / Resolution: 3.45→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16920 0 99 68 17087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01217401
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615561
X-RAY DIFFRACTIONr_angle_refined_deg0.6041.6623656
X-RAY DIFFRACTIONr_angle_other_deg0.2341.57536380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.91252170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.107568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.905102888
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.04710773
X-RAY DIFFRACTIONr_chiral_restr0.0280.22667
X-RAY DIFFRACTIONr_chiral_restr_other0.0170.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0219678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023283
X-RAY DIFFRACTIONr_nbd_refined0.1590.23570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.215729
X-RAY DIFFRACTIONr_nbtor_refined0.1650.28650
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.28845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2412
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.215
X-RAY DIFFRACTIONr_nbd_other0.1460.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.28
X-RAY DIFFRACTIONr_mcbond_it3.21715.7538701
X-RAY DIFFRACTIONr_mcbond_other3.21715.7538701
X-RAY DIFFRACTIONr_mcangle_it5.59323.62910864
X-RAY DIFFRACTIONr_mcangle_other5.59323.62910865
X-RAY DIFFRACTIONr_scbond_it2.40215.6848700
X-RAY DIFFRACTIONr_scbond_other2.40215.6848701
X-RAY DIFFRACTIONr_scangle_it4.38823.50812792
X-RAY DIFFRACTIONr_scangle_other4.38823.50812793
X-RAY DIFFRACTIONr_lrange_it8.76196.36919214
X-RAY DIFFRACTIONr_lrange_other8.76196.3719215
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.056058
X-RAY DIFFRACTIONr_ncsr_local_group_20.0690.0527045
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.087130.0501
12AX-RAY DIFFRACTIONLocal ncs0.087130.0501
23AX-RAY DIFFRACTIONLocal ncs0.069330.05011
24AX-RAY DIFFRACTIONLocal ncs0.069330.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.5390.3971400.3752995X-RAY DIFFRACTION100
3.539-3.6360.3581380.3682936X-RAY DIFFRACTION99.9675
3.636-3.7410.3641610.3432849X-RAY DIFFRACTION100
3.741-3.8550.3881310.322823X-RAY DIFFRACTION100
3.855-3.9810.3281360.2982671X-RAY DIFFRACTION100
3.981-4.1190.331110.2952628X-RAY DIFFRACTION100
4.119-4.2740.271160.2552551X-RAY DIFFRACTION100
4.274-4.4470.2751210.2542436X-RAY DIFFRACTION100
4.447-4.6430.2951390.2412330X-RAY DIFFRACTION100
4.643-4.8670.2591210.222234X-RAY DIFFRACTION100
4.867-5.1280.3041190.2342141X-RAY DIFFRACTION100
5.128-5.4360.3181090.2662007X-RAY DIFFRACTION100
5.436-5.8060.3821060.2451916X-RAY DIFFRACTION100
5.806-6.2640.33870.2571775X-RAY DIFFRACTION100
6.264-6.8510.356870.2391677X-RAY DIFFRACTION100
6.851-7.6420.255800.2151508X-RAY DIFFRACTION100
7.642-8.7890.229740.2041346X-RAY DIFFRACTION100
8.789-10.6820.25630.1841147X-RAY DIFFRACTION100
10.682-14.7710.211510.196926X-RAY DIFFRACTION100
14.771-49.780.654260.319601X-RAY DIFFRACTION100

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