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- PDB-2z8l: Crystal Structure of the Staphylococcal superantigen-like protein... -

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Basic information

Entry
Database: PDB / ID: 2z8l
TitleCrystal Structure of the Staphylococcal superantigen-like protein SSL5 at pH 4.6 complexed with sialyl Lewis X
ComponentsExotoxin 3
KeywordsSUGAR BINDING PROTEIN / OB fold / B-grasp
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sialyl-Lewis X antigen, beta anomer / PHOSPHATE ION / Exotoxin
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsBaker, H.M. / Basu, I. / Chung, M.C. / Caradoc Davies, T. / Fraser, J.D. / Baker, E.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structures of the staphylococcal toxin SSL5 in complex with sialyl Lewis X reveal a conserved binding site that shares common features with viral and bacterial sialic acid binding proteins
Authors: Baker, H.M. / Basu, I. / Chung, M.C. / Caradoc-Davies, T. / Fraser, J.D. / Baker, E.N.
History
DepositionSep 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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: Exotoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5214
Polymers24,5131
Non-polymers1,0083
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.625, 78.237, 55.276
Angle α, β, γ (deg.)90.000, 127.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exotoxin 3 / superantigen-like protein SSL5


Mass: 24513.141 Da / Num. of mol.: 1 / Fragment: UNP residues 31-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: GL10 / Gene: ssl5 / Plasmid: pET32a.3C / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: Q9ZFS6
#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-beta-D-glucopyranose / Sialyl-Lewis X antigen / beta 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, beta anomer
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_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
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE TETRASACCHARIDE SIALYL-LEWIS X IS PRESENT AS A LIGAND IN THIS STRUCTURE AND IS NOT COVALENTLY ...THE TETRASACCHARIDE SIALYL-LEWIS X IS PRESENT AS A LIGAND IN THIS STRUCTURE AND IS NOT COVALENTLY BOUND TO THE PROTEIN MOLECULE.
Sequence detailsTHE CONFLICTS BETWEEN THE SEQUENCE FOR THIS STRUCTURE AND THE DATABASE SEQUENCE ARISE FROM THE ...THE CONFLICTS BETWEEN THE SEQUENCE FOR THIS STRUCTURE AND THE DATABASE SEQUENCE ARISE FROM THE ALLELIC VARIATION BETWEEN STAPHYLOCOCCUS AUREUS STRAINS SEEN FOR SOME OF THESE SUPERANTIGEN-LIKE PROTEINS.

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20% PEG 3350, 0.2M NaH2PO4, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97892 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2006 / Details: mirror, monochromator
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionRedundancy: 7.4 % / Av σ(I) over netI: 5 / Number: 227633 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / D res high: 1.65 Å / D res low: 30.042 Å / Num. obs: 30728 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
1.651.7410010.6670.6677.4
1.741.8410010.3380.3387.4
1.841.9710010.1750.1757.4
1.972.1310010.1030.1037.4
2.132.3310010.0710.0717.4
2.332.6110010.0560.0567.5
2.613.0110010.0470.0477.5
3.013.6910010.0450.0457.5
3.695.2299.210.0450.0457.3
5.2244.1595.610.0370.0377.1
ReflectionResolution: 1.65→30.04 Å / Num. all: 30728 / Num. obs: 30702 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4497 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.78 Å
Translation1.7 Å33.78 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
REFMAC5.3.0037refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M4V

1m4v


Resolution: 1.65→28.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.434 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1538 5 %RANDOM
Rwork0.181 ---
all0.183 30790 --
obs0.183 30702 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.37 Å2
2---0.22 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 67 111 1785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221720
X-RAY DIFFRACTIONr_bond_other_d0.0010.021235
X-RAY DIFFRACTIONr_angle_refined_deg1.7442.0022306
X-RAY DIFFRACTIONr_angle_other_deg0.9132982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73623.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191511
X-RAY DIFFRACTIONr_chiral_restr0.1150.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined0.210.2278
X-RAY DIFFRACTIONr_nbd_other0.1940.21206
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2839
X-RAY DIFFRACTIONr_nbtor_other0.0940.2952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.27
X-RAY DIFFRACTIONr_mcbond_it1.8661.51240
X-RAY DIFFRACTIONr_mcbond_other0.3581.5394
X-RAY DIFFRACTIONr_mcangle_it2.09321537
X-RAY DIFFRACTIONr_scbond_it3.5173922
X-RAY DIFFRACTIONr_scangle_it4.5324.5768
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 119 -
Rwork0.255 2152 -
all-2271 -
obs--100 %
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)
10.8082-0.0623-0.29626.49891.6811.479-0.00860.2457-0.1155-0.7340.0893-0.2822-0.11770.0022-0.08070.1852-0.00580.00970.1463-0.02340.1012-0.61511.692.881
21.06390.0898-0.13612.81290.21290.6341-0.01630.1064-0.0406-0.27660.05470.0099-0.00230.0358-0.03840.1248-0.004-0.01870.1159-0.01210.1374-7.76515.11812.664
31.88520.4755-0.39133.17370.36211.07380.1307-0.07710.05970.0278-0.07290.1363-0.14880.0322-0.05780.13460.0049-0.00680.1072-0.00350.1084-5.97823.15617.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 6017 - 64
2X-RAY DIFFRACTION2AA61 - 12565 - 129
3X-RAY DIFFRACTION3AA126 - 204130 - 208

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