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- PDB-4rfb: 1.93 Angstrom Crystal Structure of Superantigen-like Protein from... -

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Basic information

Entry
Database: PDB / ID: 4rfb
Title1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.
ComponentsPutative uncharacterized protein
KeywordsTOXIN / Sialyl-Lewis X / 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. / 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Staphylococcal superantigen-like OB-fold domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: 1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.
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 25, 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.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 2.1Sep 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
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67119
Polymers102,6444
Non-polymers4,02615
Water8,485471
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,36210
Polymers51,3222
Non-polymers2,0408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-19 kcal/mol
Surface area19580 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3099
Polymers51,3222
Non-polymers1,9877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint11 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.640, 108.199, 167.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Putative uncharacterized protein


Mass: 25661.123 Da / Num. of mol.: 4 / 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)-[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.: 4
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

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Non-polymers , 5 types, 482 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.88 Å3/Da / Density % sol: 34.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEGsII (F12), 0.8M Lithium chloride, 0.1M Tris (pH 8.5), 32% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97875 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Mirrors
RadiationMonochromator: Si{1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. all: 61498 / Num. obs: 61498 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 19.3
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 3 / Num. unique all: 3076 / Rsym value: 0.552 / % 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: 1.93→28.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.359 / SU ML: 0.102
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21829 2997 5.1 %RANDOM
Rwork0.16855 ---
all0.17106 56257 --
obs0.17106 56257 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.297 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.26 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.93→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 265 471 7141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196955
X-RAY DIFFRACTIONr_bond_other_d0.0010.026801
X-RAY DIFFRACTIONr_angle_refined_deg1.6372.0289311
X-RAY DIFFRACTIONr_angle_other_deg0.722315822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7145802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.51225.25320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.993151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8671531
X-RAY DIFFRACTIONr_chiral_restr0.0990.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021416
X-RAY DIFFRACTIONr_mcbond_it1.8491.923169
X-RAY DIFFRACTIONr_mcbond_other1.8491.9193168
X-RAY DIFFRACTIONr_mcangle_it2.6972.8573984
X-RAY DIFFRACTIONr_mcangle_other2.6972.8583985
X-RAY DIFFRACTIONr_scbond_it2.8952.4273786
X-RAY DIFFRACTIONr_scbond_other2.8952.4273786
X-RAY DIFFRACTIONr_scangle_other4.5413.4685332
X-RAY DIFFRACTIONr_long_range_B_refined6.85516.77966
X-RAY DIFFRACTIONr_long_range_B_other6.7916.3897824
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 221 -
Rwork0.179 4059 -
obs-2997 99.93 %
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)
12.559-1.0092-0.18720.6923-0.11073.05920.0030.1947-0.2325-0.0233-0.1136-0.02660.21110.08240.11060.0916-0.0295-0.00960.04450.01570.0888-11.0821-17.434728.0864
21.0545-0.77220.2292.2842-2.9277.1813-0.08310.0481-0.0445-0.1011-0.069-0.11070.25580.21630.15210.0517-0.00350.01350.02070.00570.0944-7.5052-19.973530.6354
30.1341-0.1334-0.54182.10110.00192.5777-0.04470.0698-0.05030.17420.04080.28970.2421-0.32230.00390.0903-0.03510.01050.12650.03940.1807-22.5606-18.290950.2015
41.68430.2784-0.30471.51710.16261.4062-0.05930.0151-0.01330.01230.04670.10180.0244-0.16020.01250.0373-0.00540.00630.04480.02980.0737-21.8102-13.175844.3898
56.4177-0.87732.21090.1334-0.09714.2747-0.0346-0.0811-0.06230.02510.03830.00860.40540.2111-0.00370.12540.04480.03860.09650.02280.09040.07542.174918.749
61.8865-1.0827-0.10263.024-0.83954.3645-0.0412-0.01-0.03530.20870.0370.1151-0.0045-0.29880.00420.0567-0.0170.02850.14410.0280.066-22.9728-1.958315.4715
70.93860.8760.53822.61870.79261.2106-0.03110.04460.1266-0.2254-0.0042-0.0094-0.1496-0.03960.03530.07660.0160.02950.07140.03790.0526-11.279712.865516.5157
81.2245-0.0080.11471.980.3112.17510.00940.02130.15790.0261-0.0002-0.0787-0.13210.117-0.00920.05360.01140.01950.03790.02340.0484-5.763714.038323.495
91.5275-0.1361-0.19530.86110.18562.21660.0232-0.19680.10550.1011-0.02670.0211-0.0056-0.26960.00350.0301-0.03620.00160.1277-0.02580.0609-22.37760.799180.4095
101.2631-0.3368-0.21982.69820.43521.96770.0097-0.1703-0.15380.2378-0.0222-0.20410.3012-0.01460.01250.0788-0.0307-0.03780.12050.02320.0727-14.6102-11.676480.4335
113.53391.92840.42962.68850.38562.6152-0.02810.0937-0.2367-0.10780.034-0.18270.31260.1518-0.00590.06330.0228-0.02210.0642-0.00520.0993-7.0143-14.845673.1001
123.50470.4809-0.61072.07130.45521.81570.11140.0102-0.2216-0.0266-0.0489-0.12750.2795-0.0377-0.06250.0892-0.0201-0.04390.1009-0.0070.0597-12.0672-13.759771.6732
131.9510.54580.38741.0971-0.29052.47220.0592-0.00870.33940.0309-0.1221-0.0553-0.21670.02880.06290.1036-0.00510.00710.0508-0.0210.1533-16.099516.721766.6354
140.81561.0389-1.38092.0163-2.62295.1188-0.096-0.03090.17610.0160.0179-0.1258-0.19410.02940.07820.1848-0.002-0.02120.0935-0.03010.2497-16.220419.511462.0018
152.09020.27590.12882.2050.43812.0698-0.05470.10210.1041-0.3065-0.03520.2486-0.105-0.21550.08990.11690.0277-0.05310.05530.02370.1008-27.72749.736347.5855
161.2284-0.13840.67121.76430.57412.23860.04870.0020.1183-0.1496-0.07040.15290.0238-0.03330.02170.10320.0096-0.00440.02370.01910.0641-22.17518.127150.105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 91
2X-RAY DIFFRACTION2A92 - 128
3X-RAY DIFFRACTION3A129 - 163
4X-RAY DIFFRACTION4A164 - 231
5X-RAY DIFFRACTION5B38 - 52
6X-RAY DIFFRACTION6B53 - 96
7X-RAY DIFFRACTION7B97 - 158
8X-RAY DIFFRACTION8B159 - 231
9X-RAY DIFFRACTION9C39 - 97
10X-RAY DIFFRACTION10C98 - 167
11X-RAY DIFFRACTION11C168 - 201
12X-RAY DIFFRACTION12C202 - 231
13X-RAY DIFFRACTION13D39 - 96
14X-RAY DIFFRACTION14D97 - 130
15X-RAY DIFFRACTION15D131 - 205
16X-RAY DIFFRACTION16D206 - 231

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