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- PDB-4rgt: 2.0 Angstrom Crystal Structure of Superantigen-like Protein from ... -

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Entry
Database: PDB / ID: 4rgt
Title2.0 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with 3-N-Acetylneuraminyl-N-acetyllactosamine.
ComponentsPutative uncharacterized protein
KeywordsTOXIN / 3-N-Acetylneuraminyl-N-acetyllactosamine / Superantigen-like Protein / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
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
3'-sialyl-N-acetyllactosamine / DI(HYDROXYETHYL)ETHER / Superantigen-like protein SSL6
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. ...Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.0 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with 3-N-Acetylneuraminyl-N-acetyllactosamine.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)52,7785
Polymers51,3222
Non-polymers1,4553
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.832, 141.832, 41.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Putative uncharacterized protein


Mass: 25661.123 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_00391 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q2G1S5
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: Classics II (D3), 0.1M HEPES (pH 7.0), 30% (v/v) Jeffamine ED-2001., 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: Aug 25, 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: 2→30 Å / Num. all: 32916 / Num. obs: 32916 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 25.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1606 / Rsym value: 0.627 / % 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: 3V05

3v05


Resolution: 2→29.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.238 / SU ML: 0.131
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24704 1669 5.1 %RANDOM
Rwork0.19786 ---
all0.20028 31234 --
obs0.20028 31234 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.38 Å20 Å2
2--0.38 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 99 247 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193476
X-RAY DIFFRACTIONr_bond_other_d0.0010.023398
X-RAY DIFFRACTIONr_angle_refined_deg1.6062.0184651
X-RAY DIFFRACTIONr_angle_other_deg0.70837914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5355405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93425.155161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94315736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7581516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
X-RAY DIFFRACTIONr_mcbond_it1.7092.0421599
X-RAY DIFFRACTIONr_mcbond_other1.7092.041598
X-RAY DIFFRACTIONr_mcangle_it2.493.0312011
X-RAY DIFFRACTIONr_mcangle_other2.4893.0322012
X-RAY DIFFRACTIONr_scbond_it2.372.4351877
X-RAY DIFFRACTIONr_scbond_other2.362.4351877
X-RAY DIFFRACTIONr_scangle_other3.6173.5442643
X-RAY DIFFRACTIONr_long_range_B_refined8.37818.1214081
X-RAY DIFFRACTIONr_long_range_B_other8.3317.5553994
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 120 -
Rwork0.266 2250 -
obs-2250 99.25 %
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)
16.70825.362-7.096911.2373-3.39028.2656-0.0882-0.655-0.63471.1018-0.7360.05930.4480.60770.82420.3822-0.03370.13290.42690.11840.1642-11.095652.545713.0365
21.22051.60940.38143.46661.45841.3267-0.19290.1885-0.4251-0.29060.259-0.60450.25230.3304-0.06620.34990.02120.1690.2978-0.05750.2733-4.259546.2862-8.4866
32.560.60610.11944.29641.66592.8216-0.26070.3097-0.3293-0.4190.2534-0.5804-0.31510.4210.00740.2382-0.06830.19090.3197-0.01320.2272-3.142850.9781-9.0777
44.32243.23651.32136.61172.45773.28360.0237-0.51740.22040.3201-0.1985-0.0918-0.07010.21460.17480.1253-0.06550.00980.23660.00710.0844-2.796966.80586.1095
53.6982.809-0.22587.4942-5.24898.6201-0.0817-0.51011.06030.19410.05510.7546-0.5249-0.14730.02660.1923-0.0435-0.01190.2238-0.09250.3538-10.937869.77922.6047
64.92952.15420.60045.06521.2651.9788-0.2467-0.2920.58340.0067-0.11870.447-0.07950.1190.36540.1427-0.05660.03260.173-0.02710.1611-9.893765.2371.6338
73.03710.09820.53981.5947-0.53471.9971-0.2609-0.0868-0.61240.05350.1427-0.13330.1687-0.00060.11820.2201-0.02190.19830.1073-0.00330.2502-23.246238.32052.2075
85.593-1.3894-1.5263.106-0.36412.7336-0.35580.0448-0.67140.02520.1462-0.07130.258-0.00290.20960.228-0.04520.18350.07940.0090.2656-24.992136.88922.2023
94.7816-1.5802-0.09154.4984-7.219414.6-0.04630.3391-0.28490.02820.180.5291-0.0799-0.0474-0.13370.3744-0.19190.02580.41390.07050.4593-47.007148.3861-9.3874
104.5222-0.24511.69961.9471-0.40371.1211-0.42590.195-0.8393-0.18810.38430.12370.0255-0.04790.04160.3994-0.15410.19770.2672-0.09220.4686-39.03342.3085-5.9773
115.62521.4963-1.50373.87280.73917.4858-0.60140.76850.0342-0.43330.4652-0.0199-0.1566-0.07660.13620.1789-0.16750.04240.189-0.00370.0818-37.380952.1377-10.1546
124.7195-0.52660.81722.5256-1.1191.7162-0.74680.3651-0.0385-0.16230.3326-0.01570.11220.00370.41420.2751-0.17040.10030.1759-0.02130.1794-35.768150.6635-6.3331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 46
2X-RAY DIFFRACTION2A47 - 88
3X-RAY DIFFRACTION3A89 - 130
4X-RAY DIFFRACTION4A131 - 182
5X-RAY DIFFRACTION5A183 - 198
6X-RAY DIFFRACTION6A199 - 231
7X-RAY DIFFRACTION7B38 - 96
8X-RAY DIFFRACTION8B97 - 125
9X-RAY DIFFRACTION9B126 - 148
10X-RAY DIFFRACTION10B149 - 176
11X-RAY DIFFRACTION11B177 - 201
12X-RAY DIFFRACTION12B202 - 231

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