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- PDB-5u75: The structure of Staphylococcal Enterotoxin-like X (SElX), a Uniq... -

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Basic information

Entry
Database: PDB / ID: 5u75
TitleThe structure of Staphylococcal Enterotoxin-like X (SElX), a Unique Superantigen
ComponentsEnterotoxin-like toxin X
KeywordsTOXIN / Staphylococcal Superantigen / Sialyl Lewis X / immune evasion molecule
Function / homologyStaphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / extracellular region / Sialyl-Lewis X antigen, alpha anomer / Enterotoxin-like toxin X
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsTing, Y.T. / Young, P.G. / Langley, R.J. / Baker, H. / Fraser, J.D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
New Zealand Health research Council12/1111 New Zealand
CitationJournal: PLoS Pathog. / Year: 2017
Title: Staphylococcal enterotoxin-like X (SElX) is a unique superantigen with functional features of two major families of staphylococcal virulence factors.
Authors: Langley, R.J. / Ting, Y.T. / Clow, F. / Young, P.G. / Radcliff, F.J. / Choi, J.M. / Sequeira, R.P. / Holtfreter, S. / Baker, H. / Fraser, J.D.
History
DepositionDec 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enterotoxin-like toxin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2402
Polymers19,4191
Non-polymers8211
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.141, 92.141, 53.418
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Enterotoxin-like toxin X


Mass: 19418.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: JSNZ / Gene: selX, selx8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0Z026
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Sialyl-Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 820.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Sialyl-Lewis X antigen, alpha anomer
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 63.51 % / Description: Rods
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: SEIX (10 mg/ml), SLeX (5 mM), PEG 3350 (24%), Tri-Lithium citrate (250 mM)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 2013 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→18.85 Å / Num. obs: 28745 / % possible obs: 94.4 % / Redundancy: 15.6 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/av σ(I): 17.9 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.66-1.7514.91.9420.40.522187.6
1.75-1.8615.71.4750.50.728192.6
1.86-1.9915.70.7810.908193.6
1.99-2.1515.70.4331.80.969194.7
2.15-2.3515.70.2872.70.985195.9
2.35-2.6315.80.19240.992196.5
2.63-3.0415.80.1126.70.998197.6
3.04-3.7215.60.05413.50.999198.5
3.72-5.2615.60.03320.81199.2
5.26-18.84715.20.03221.91197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
PHASER2.5.2phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DXG

4dxg


Resolution: 1.66→18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0.083 / SU B: 2.013 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0808 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 1456 5.1 %RANDOM
Rwork0.1851 ---
obs0.1866 27279 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.68 Å2 / Biso mean: 21.542 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.13 Å20 Å2
2---0.27 Å20 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 1.66→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 56 147 1350
Biso mean--25.32 31.75 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191270
X-RAY DIFFRACTIONr_bond_other_d0.0020.021187
X-RAY DIFFRACTIONr_angle_refined_deg1.38521735
X-RAY DIFFRACTIONr_angle_other_deg0.88732736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40324.75461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.72915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.472158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_mcbond_it1.1422.047597
X-RAY DIFFRACTIONr_mcbond_other1.1352.041596
X-RAY DIFFRACTIONr_mcangle_it1.7643.052752
LS refinement shellResolution: 1.66→1.7 Å
RfactorNum. reflection% reflection
Rfree0.311 95 5 %
Rwork0.333 1712 -
obs--82.55 %

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