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- PDB-6ucd: The crystal structure of Staphylococcus aureus super antigen-like... -

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Basic information

Entry
Database: PDB / ID: 6ucd
TitleThe crystal structure of Staphylococcus aureus super antigen-like protein SSL10
ComponentsExotoxin
KeywordsTOXIN / Complement coagulation / IgG / Staphylococcus aureus / immune evasion
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 / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Enterotoxin
Similarity search - Domain/homology
Exotoxin / Staphylococcal superantigen-like 10
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsPatel, D. / Young, P.G. / Bunker, R.D. / Baker, E.N. / Fraser, J.D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)12/1111 New Zealand
CitationJournal: To Be Published
Title: The crystal structure of Staphylococcus aureus super antigen-like protein SSL10
Authors: Patel, D. / Hou, W. / Langley, R.J. / Young, P.G. / Ivanovic, I. / Bunker, R.D. / Baker, E.N. / Fraser, J.D.
History
DepositionSep 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exotoxin
B: Exotoxin


Theoretical massNumber of molelcules
Total (without water)46,5302
Polymers46,5302
Non-polymers00
Water00
1
A: Exotoxin


Theoretical massNumber of molelcules
Total (without water)23,2651
Polymers23,2651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exotoxin


Theoretical massNumber of molelcules
Total (without water)23,2651
Polymers23,2651
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.550, 91.550, 46.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Exotoxin / Superantigen-like protein / Superantigen-like protein SSL10 / exotoxin 14


Mass: 23265.064 Da / Num. of mol.: 2 / Fragment: UNP residues 31-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: tst, set14_2, BTN44_10650, EP54_13120, ER624_09120, HMPREF3211_02406, M1K003_2331, NCTC10654_00508, NCTC13131_05891, RK64_02640
Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3)pLysS / References: UniProt: A0A0D6W7J6, UniProt: Q2G2X7*PLUS

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG1500, 8% MPD, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 2010
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→64.74 Å / Num. obs: 8204 / % possible obs: 89.5 % / Redundancy: 2.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.081 / Rrim(I) all: 0.147 / Net I/av σ(I): 6.8 / Net I/σ(I): 6.8
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1139 / CC1/2: 0.44 / Rpim(I) all: 0.385 / Rrim(I) all: 0.683 / % possible all: 87.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V1O

1v1o


Resolution: 2.85→45.78 Å / Cross valid method: THROUGHOUT
Details: TWIN DETAILS NUMBER OF TWIN DOMAINS : 2 TWIN DOMAIN : 1 TWIN OPERATOR : H, K, L TWIN FRACTION : 0.486 TWIN DOMAIN : 2 TWIN OPERATOR : -K, -H, -L TWIN FRACTION : 0.514
RfactorNum. reflection% reflectionSelection details
Rfree0.281 413 5 %Random
Rwork0.246 ---
obs0.248 7778 88.86 %-
Displacement parametersBiso max: 78.95 Å2 / Biso mean: 37.304 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 0 0 2733
LS refinement shellResolution: 2.85→2.92 Å
RfactorNum. reflection% reflection
Rfree0.376 35 5 %
Rwork0.322 543 -
obs--85.63 %

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