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- PDB-6en3: Crystal structure of full length EndoS from Streptococcus pyogene... -

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Basic information

Entry
Database: PDB / ID: 6en3
TitleCrystal structure of full length EndoS from Streptococcus pyogenes in complex with G2 oligosaccharide.
ComponentsEndo-beta-N-acetylglucosaminidase F2,Multifunctional-autoprocessing repeats-in-toxin
KeywordsHYDROLASE / endoglycosidase/immunoglobulin/carbohydrate/endo-beta-N-acetylglucos aminidase
Function / homology
Function and homology information


CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...CoA-dependent peptidyl-lysine N6-palmitoyltransferase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / host cell cytosol / ligase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / cysteine-type peptidase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / actin filament organization / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / carbohydrate metabolic process / lipid binding / host cell plasma membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Endo-beta-N-acetylglucosaminidase F2, Ig-like domain / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / : / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat ...: / Endo-beta-N-acetylglucosaminidase F2, Ig-like domain / Actin cross-linking domain / Actin cross-linking domain / Actin cross-linking (ACD) domain profile. / : / C-terminal repeat from RTX toxins / : / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Endo-beta-N-acetylglucosaminidase F2 / Multifunctional-autoprocessing repeats-in-toxin
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsTrastoy, B. / Klontz, E.H. / Orwenyo, J. / Marina, A. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S.
Authors: Trastoy, B. / Klontz, E. / Orwenyo, J. / Marina, A. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Jan 17, 2024Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase F2,Multifunctional-autoprocessing repeats-in-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,8974
Polymers133,3601
Non-polymers1,5373
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint11 kcal/mol
Surface area45210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.640, 90.080, 104.370
Angle α, β, γ (deg.)90.00, 110.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase F2,Multifunctional-autoprocessing repeats-in-toxin / MARTX


Mass: 133360.219 Da / Num. of mol.: 1 / Mutation: D233A, L235E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria), (gene. exp.) Vibrio cholerae (bacteria)
Gene: endoS, M1GAS476_1618, rtxA, rtx, VC_1451 / Production host: Escherichia coli (E. coli)
References: UniProt: J7M8R4, UniProt: Q9KS12, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Sodium HEPES/MOPS pH 7.5, 100 mM aminoacids (L-Na-Glutamate, alanine (racemic), glycine, lysine HCL (racemic), serine (racemic)), 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 2.9→45.04 Å / Num. obs: 118762 / % possible obs: 98.8 % / Redundancy: 4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3.007 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.781 / CC1/2: 0.852 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NUZ

4nuz


Resolution: 2.903→45.04 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2900 5.02 %
Rwork0.2093 --
obs0.2109 57811 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.903→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 100 7 7451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037593
X-RAY DIFFRACTIONf_angle_d0.57810276
X-RAY DIFFRACTIONf_dihedral_angle_d13.5582895
X-RAY DIFFRACTIONf_chiral_restr0.0421161
X-RAY DIFFRACTIONf_plane_restr0.0041313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.903-2.95060.3861260.37292398X-RAY DIFFRACTION91
2.9506-3.00140.37841380.36172622X-RAY DIFFRACTION100
3.0014-3.0560.39531400.3312643X-RAY DIFFRACTION99
3.056-3.11480.43041410.32872674X-RAY DIFFRACTION99
3.1148-3.17830.33811360.31072549X-RAY DIFFRACTION100
3.1783-3.24740.30261410.29962692X-RAY DIFFRACTION100
3.2474-3.32290.34781370.29562616X-RAY DIFFRACTION99
3.3229-3.4060.32791390.27372644X-RAY DIFFRACTION100
3.406-3.49810.25971390.24722668X-RAY DIFFRACTION100
3.4981-3.60090.24431400.2382640X-RAY DIFFRACTION100
3.6009-3.71710.25561390.21852668X-RAY DIFFRACTION100
3.7171-3.84990.27091380.22642604X-RAY DIFFRACTION99
3.8499-4.0040.24591400.212568X-RAY DIFFRACTION99
4.004-4.18610.22211400.18772653X-RAY DIFFRACTION99
4.1861-4.40660.21081380.17012616X-RAY DIFFRACTION99
4.4066-4.68240.16411360.16162543X-RAY DIFFRACTION96
4.6824-5.04350.19911370.1632580X-RAY DIFFRACTION98
5.0435-5.55020.20461350.17232622X-RAY DIFFRACTION98
5.5502-6.35140.24331430.18492623X-RAY DIFFRACTION100
6.3514-7.99480.20211360.18012656X-RAY DIFFRACTION100
7.9948-45.04540.16931410.14862632X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67950.1702-0.21781.6381-0.29863.51750.06940.00410.1717-0.0275-0.08650.3164-0.1379-0.3652-0.00060.45270.0180.02220.4601-0.04820.602369.6943155.0581274.2416
20.1362-0.32030.04430.445-1.02971.6550.06090.11260.0517-0.0399-0.1703-0.0219-0.00050.401400.5892-0.0170.02370.64880.01470.60587.7916164.329242.3533
33.46151.43020.39130.83220.59611.48340.3231-0.267-0.47560.273-0.3373-0.08740.4798-0.33050.00030.7867-0.0891-0.01320.6062-0.00530.622842.0122161.193209.4609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 346 )
2X-RAY DIFFRACTION2chain 'A' and (resid 347 through 687 )
3X-RAY DIFFRACTION3chain 'A' and (resid 688 through 987 )

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