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- PDB-2rdh: Crystal structure of Staphylococcal Superantigen-Like protein 11 -

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Basic information

Entry
Database: PDB / ID: 2rdh
TitleCrystal structure of Staphylococcal Superantigen-Like protein 11
ComponentsSuperantigen-like protein 11
KeywordsTOXIN / OB fold / beta grasp
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/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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 ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp 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
PHOSPHATE ION / Superantigen-like protein 11
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChung, M.C. / Wines, B.D. / Baker, H. / Langley, R.J. / Baker, E.N. / Fraser, J.D.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: The crystal structure of staphylococcal superantigen-like protein 11 in complex with sialyl Lewis X reveals the mechanism for cell binding and immune inhibition
Authors: Chung, M.C. / Wines, B.D. / Baker, H. / Langley, R.J. / Baker, E.N. / Fraser, J.D.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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: Superantigen-like protein 11
B: Superantigen-like protein 11
C: Superantigen-like protein 11
D: Superantigen-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1529
Polymers90,7494
Non-polymers4035
Water13,277737
1
A: Superantigen-like protein 11
C: Superantigen-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5644
Polymers45,3752
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
MethodPISA
2
B: Superantigen-like protein 11
D: Superantigen-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5875
Polymers45,3752
Non-polymers2133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.391, 98.152, 79.515
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superantigen-like protein 11


Mass: 22687.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: US6610 / Gene: SSL11 / Plasmid: pET32a-3C / Production host: Escherichia coli (E. coli) / Strain (production host): AD494 / References: UniProt: A8E1U5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M PEG3350, 0.2M NaH2PO4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.7→30.89 Å / Num. obs: 86026 / % possible obs: 94 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.028
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3 / Num. unique all: 6500 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M4V

1m4v


Resolution: 1.7→30.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.834 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23878 4300 5 %RANDOM
Rwork0.1923 ---
obs0.19461 85991 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.391 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.05 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 21 737 6930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226382
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9518611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7825.159347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.007151227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8551542
X-RAY DIFFRACTIONr_chiral_restr0.1040.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024834
X-RAY DIFFRACTIONr_nbd_refined0.1950.22718
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2724
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.230
X-RAY DIFFRACTIONr_mcbond_it0.8591.53812
X-RAY DIFFRACTIONr_mcangle_it1.48426210
X-RAY DIFFRACTIONr_scbond_it2.36832606
X-RAY DIFFRACTIONr_scangle_it3.6864.52390
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 226 -
Rwork0.304 4328 -
obs--67.75 %
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)
10.40890.09550.03590.6663-0.76472.44960.0858-0.0036-0.0237-0.0138-0.0810.05050.1882-0.013-0.0048-0.0808-0.02220.0029-0.0530.0073-0.0538.1350.1533.892
21.22-0.11981.25990.5019-0.15812.780.0220.091-0.1144-0.08570.02520.04670.03030.0885-0.0472-0.10940.0406-0.0108-0.03360.0178-0.0473-8.35413.46635.593
31.68020.1634-0.69461.6644-0.61732.57370.096-0.06540.210.2227-0.1477-0.0334-0.15850.10320.0517-0.1104-0.0289-0.004-0.090.0109-0.046618.01925.1842.219
40.2265-0.0322-0.14231.0256-0.8011.2378-0.0048-0.0111-0.001-0.0173-0.00390.11520.02270.00490.0087-0.0669-0.0218-0.0258-0.00810.0171-0.0128-21.02937.55234.153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 276 - 27
2X-RAY DIFFRACTION1AA28 - 5228 - 52
3X-RAY DIFFRACTION1AA53 - 8853 - 88
4X-RAY DIFFRACTION1AA89 - 12789 - 127
5X-RAY DIFFRACTION1AA128 - 196128 - 196
6X-RAY DIFFRACTION2BB6 - 276 - 27
7X-RAY DIFFRACTION2BB28 - 5228 - 52
8X-RAY DIFFRACTION2BB53 - 8853 - 88
9X-RAY DIFFRACTION2BB89 - 12789 - 127
10X-RAY DIFFRACTION2BB128 - 196128 - 196
11X-RAY DIFFRACTION3CC6 - 276 - 27
12X-RAY DIFFRACTION3CC28 - 5228 - 52
13X-RAY DIFFRACTION3CC53 - 8853 - 88
14X-RAY DIFFRACTION3CC89 - 12789 - 127
15X-RAY DIFFRACTION3CC128 - 196128 - 196
16X-RAY DIFFRACTION4DD6 - 276 - 27
17X-RAY DIFFRACTION4DD28 - 5228 - 52
18X-RAY DIFFRACTION4DD53 - 8853 - 88
19X-RAY DIFFRACTION4DD89 - 12789 - 127
20X-RAY DIFFRACTION4DD128 - 186128 - 186

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