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- PDB-6lwt: Crystal structure of Staphylococcal Superantigen-Like protein 10 -

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Basic information

Entry
Database: PDB / ID: 6lwt
TitleCrystal structure of Staphylococcal Superantigen-Like protein 10
ComponentsSuperantigen-like protein SSL10
KeywordsIMMUNE SYSTEM / Staphylococcal 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. / 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
Superantigen-like protein SSL10 / Staphylococcal superantigen-like 10
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNan, J. / Chengliang, W. / Tianrong, H.
CitationJournal: To Be Published
Title: Crystal structure of Staphylococcal Superantigen-Like protein 10
Authors: Nan, J. / Chengliang, W. / Tianrong, H.
History
DepositionFeb 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Superantigen-like protein SSL10
B: Superantigen-like protein SSL10


Theoretical massNumber of molelcules
Total (without water)48,9352
Polymers48,9352
Non-polymers00
Water1,02757
1
A: Superantigen-like protein SSL10


Theoretical massNumber of molelcules
Total (without water)24,4671
Polymers24,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superantigen-like protein SSL10


Theoretical massNumber of molelcules
Total (without water)24,4671
Polymers24,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.243, 71.211, 140.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Superantigen-like protein SSL10


Mass: 24467.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: E5491_02145, FAF10_06335, FAF13_10025, FAF15_01065, FAF17_11070
Production host: Escherichia coli (E. coli) / References: UniProt: A0A4T9YNX5, UniProt: Q2G2X7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→70.33 Å / Num. obs: 33517 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 1.06 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.936.60.29416440.9450.1250.321.074100
1.93-1.976.60.25616490.9440.1090.2781.086100
1.97-2.016.50.22816480.9580.0970.2481.079100
2.01-2.056.50.20616380.9670.0880.2251.1100
2.05-2.096.40.19816690.9560.0850.2161.107100
2.09-2.1460.17316330.9640.0770.191.085100
2.14-2.196.20.16216490.9740.0710.1771.068100
2.19-2.256.70.18716530.9720.080.2041.119100
2.25-2.326.70.14416490.9780.060.1561.077100
2.32-2.396.60.13616560.9830.0580.1481.105100
2.39-2.486.40.1316490.9830.0560.1421.068100
2.48-2.586.20.12116940.9820.0530.1321.027100
2.58-2.76.20.11316430.9880.0490.1241.081100
2.7-2.846.70.09816790.9890.0410.1071.058100
2.84-3.026.60.09116860.9920.0380.0990.999100
3.02-3.256.50.08416720.9910.0360.0911.041100
3.25-3.586.10.07717070.9930.0340.0841.025100
3.58-4.096.70.07417120.9940.030.080.98199.9
4.09-5.166.10.07317410.9930.0320.080.956100
5.16-5060.07918460.9910.0360.0871.07699.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.428 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1632 4.9 %RANDOM
Rwork0.2094 ---
obs0.2111 31821 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.3 Å2 / Biso mean: 30.971 Å2 / Biso min: 15.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-0 Å2
2---0.94 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 0 57 3184
Biso mean---27.26 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193182
X-RAY DIFFRACTIONr_bond_other_d0.0020.023214
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9824238
X-RAY DIFFRACTIONr_angle_other_deg0.87737430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76624.247146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79515676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 118 -
Rwork0.242 2260 -
all-2378 -
obs--97.86 %

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