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- PDB-4rco: 1.9 Angstrom Crystal Structure of Superantigen-like Protein, Exot... -

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Entry
Database: PDB / ID: 4rco
Title1.9 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.
ComponentsPutative uncharacterized protein
KeywordsTOXIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / superantigen-like protein
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. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal ...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. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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, alpha anomer / Staphylococcal superantigen-like 4
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E. / Halavaty, A. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. ...Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E. / Halavaty, A. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.9 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E. / Halavaty, A. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for ...Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E. / Halavaty, A. / Dubrovska, I. / Flores, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0977
Polymers66,3492
Non-polymers1,7485
Water8,377465
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0313
Polymers33,1751
Non-polymers8562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0664
Polymers33,1751
Non-polymers8923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-12 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.983, 88.904, 153.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 33174.586 Da / Num. of mol.: 2 / Fragment: Superantigen-like Protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_00389 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q2G1S8
#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.: 2
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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDUE TO DEGRADATION OF THE PROTEIN IN THE CRYSTAL ONLY RESIDUES 116 TO 308 WERE OBSERVED AND ...DUE TO DEGRADATION OF THE PROTEIN IN THE CRYSTAL ONLY RESIDUES 116 TO 308 WERE OBSERVED AND REPORTED IN THE SEQRES RECORDS

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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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 6.6 mg/ml, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 2.4mM LewisX, 5mM BME; Screen: JCSG+ (G6), 0.24M Sodium malonate (pH 7.0), 20%(w/v) PEG 3350., VAPOR DIFFUSION, ...Details: Protein: 6.6 mg/ml, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 2.4mM LewisX, 5mM BME; Screen: JCSG+ (G6), 0.24M Sodium malonate (pH 7.0), 20%(w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2014 / Details: beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 37801 / Num. obs: 37801 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 26.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1815 / Rsym value: 0.459 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3URY

3ury


Resolution: 1.9→29.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.63 / SU ML: 0.095
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 1887 5 %RANDOM
Rwork0.17174 ---
all0.17389 35792 --
obs0.17389 35792 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.53 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 115 465 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193513
X-RAY DIFFRACTIONr_bond_other_d0.0010.023468
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0024753
X-RAY DIFFRACTIONr_angle_other_deg0.68338039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2045428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28525.562160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13715705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4461513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02763
X-RAY DIFFRACTIONr_mcbond_it1.9142.2121641
X-RAY DIFFRACTIONr_mcbond_other1.9132.2111640
X-RAY DIFFRACTIONr_mcangle_it2.8053.3032082
X-RAY DIFFRACTIONr_mcangle_other2.8043.3032083
X-RAY DIFFRACTIONr_scbond_it2.6462.6661872
X-RAY DIFFRACTIONr_scbond_other2.6462.6661872
X-RAY DIFFRACTIONr_scangle_other4.1993.872670
X-RAY DIFFRACTIONr_long_range_B_refined8.19320.6624245
X-RAY DIFFRACTIONr_long_range_B_other8.08419.614041
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 126 -
Rwork0.231 2543 -
obs--99.96 %
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)
11.68880.3471-0.65841.092-0.53332.4336-0.20250.2720.2407-0.23190.13130.1447-0.1772-0.1010.07120.1845-0.0634-0.06610.06030.04330.1032-1.0592-14.851929.6257
23.48591.259-3.79242.1037-0.87567.2149-0.2550.0839-0.1679-0.09430.09830.1730.3989-0.1520.15680.1364-0.00190.07060.010.0060.1164-2.5113-35.531542.064
32.37210.6163-0.23611.48860.17870.9047-0.201-0.0356-0.1401-0.04060.05680.02540.0741-0.00440.14420.08570.01920.03350.05770.0090.1066-1.6081-26.601144.5374
40.8820.1615-0.3690.8577-0.77983.2580.0643-0.1578-0.06020.247-0.0858-0.1259-0.0309-0.14460.02140.1015-0.0332-0.05590.12070.05270.0687.0923-4.03625.9919
53.32632.2045-2.50574.0308-1.81582.20990.04710.0133-0.2488-0.1097-0.1516-0.35080.1686-0.07640.10450.1455-0.0114-0.02230.13310.04280.157410.3441-6.0075-19.7637
61.49060.1712-0.20411.6872-0.47371.6607-0.0060.00050.01160.0159-0.0784-0.1189-0.0195-0.11180.08440.02880.0057-0.02380.12710.03810.07857.5398-0.1056-12.3266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A117 - 202
2X-RAY DIFFRACTION2A203 - 238
3X-RAY DIFFRACTION3A239 - 308
4X-RAY DIFFRACTION4B117 - 204
5X-RAY DIFFRACTION5B205 - 236
6X-RAY DIFFRACTION6B237 - 308

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