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- PDB-3v05: 2.4 Angstrom Crystal Structure of Superantigen-like Protein from ... -

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Entry
Database: PDB / ID: 3v05
Title2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.
ComponentsSuperantigen-like Protein
KeywordsTOXIN / Center for Structural Genomics of Infectious Diseases / CSGID / 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 / 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
Staphylococcal superantigen-like OB-fold domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. ...Minasov, G. / Halavaty, A. / Shuvalova, L. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superantigen-like Protein
B: Superantigen-like Protein
C: Superantigen-like Protein
D: Superantigen-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7156
Polymers102,6444
Non-polymers712
Water3,999222
1
A: Superantigen-like Protein
B: Superantigen-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3583
Polymers51,3222
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-20 kcal/mol
Surface area18420 Å2
MethodPISA
2
C: Superantigen-like Protein
D: Superantigen-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3583
Polymers51,3222
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-19 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.640, 106.504, 162.085
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Superantigen-like Protein


Mass: 25661.123 Da / Num. of mol.: 4 / Fragment: UNP residues 31-231
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): BL21 / References: UniProt: Q2G1S5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 34.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PACT (D6), 0.1M MMT buffer (pH 9.0), 25% (w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2011 / 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: 2.4→30 Å / Num. all: 31397 / Num. obs: 31397 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1519 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3URY

3ury


Resolution: 2.4→29.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.283 / SU ML: 0.134
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25967 1569 5 %RANDOM
Rwork0.19486 ---
all0.19809 29519 --
obs0.19809 29519 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å20 Å2
2--1.46 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6357 0 2 222 6581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226490
X-RAY DIFFRACTIONr_bond_other_d0.0010.024755
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9878650
X-RAY DIFFRACTIONr_angle_other_deg0.708311650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3635762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.47725.147307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.522151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.541528
X-RAY DIFFRACTIONr_chiral_restr0.070.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026946
X-RAY DIFFRACTIONr_gen_planes_other00.021242
X-RAY DIFFRACTIONr_mcbond_it0.6741.53798
X-RAY DIFFRACTIONr_mcbond_other0.1621.51566
X-RAY DIFFRACTIONr_mcangle_it1.26426144
X-RAY DIFFRACTIONr_scbond_it2.11232692
X-RAY DIFFRACTIONr_scangle_it3.3094.52506
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 119 -
Rwork0.192 2129 -
obs-2129 99.78 %
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)
12.6309-0.59710.0312.6338-0.56182.3906-0.0329-0.20930.11740.10150.1135-0.1289-0.01250.1416-0.08060.01780.0008-0.00720.0868-0.01670.014522.746-0.6004-5.4957
220.8382-5.17568.18165.2487-1.8447.2033-1.1194-0.9740.99730.41140.65710.0004-1.3104-0.68740.46220.50270.03280.01630.1681-0.11380.503210.450122.7314-5.8975
38.2476-0.858-0.20223.6058-0.28983.4-0.20370.16850.7232-0.12340.15910.2077-0.6149-0.10230.04460.20870.0145-0.02420.01570.02870.17111.512814.0805-11.363
42.7054-0.311-0.18112.647-0.59092.82880.0435-0.009-0.1095-0.0335-0.02380.28490.0191-0.0509-0.01970.00370.0044-0.00080.00970.00710.076216.0854-13.7671-21.3013
514.58165.6264-2.88555.6643-0.97285.2327-0.67680.7305-0.0881-1.52040.2491-0.27710.18450.47120.42770.55390.05190.03580.34410.07220.153427.8862-9.8425-44.373
64.82550.4064-0.22653.2115-0.6053.2525-0.04520.2760.2826-0.4205-0.0295-0.0874-0.17590.2460.07470.0907-0.01340.00750.06090.03340.02627.0281-5.2066-34.9018
74.83960.04481.19381.8825-0.17622.416-0.04460.28160.315-0.1357-0.1778-0.22580.01840.25770.22230.07930.04680.02180.06920.02970.209634.5835-32.0709-25.4795
823.68957.24352.9854.0580.95295.6706-0.91611.59781.0043-1.08510.24820.1954-0.38010.63810.66790.68930.1172-0.00510.78950.28160.356225.9531-29.2299-48.5405
99.7814-0.75871.41284.3352-0.0865.01880.12121.2906-0.0865-0.6379-0.08020.04940.31280.2124-0.0410.29170.0889-0.0610.2448-0.03260.052923.3351-37.2909-40.5351
104.1798-1.52630.06473.11240.4652.33990.0716-0.13130.1191-0.1671-0.01610.0902-0.068-0.142-0.05550.08430.0257-0.00720.12640.00550.014326.4432-47.9123-12.317
1122.0656-5.5276-6.89327.41852.78177.8654-0.28860.1398-0.8850.0640.2680.13351.18230.4770.02060.49330.0681-0.10630.15880.04040.274234.8934-72.4542-16.6656
126.9715-1.2752-0.17333.65631.05954.47520.19780.1713-0.5259-0.3086-0.0464-0.14930.35170.1565-0.15140.26640.0509-0.01420.0717-0.01280.0635.393-62.7184-21.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 125
2X-RAY DIFFRACTION2A126 - 156
3X-RAY DIFFRACTION3A157 - 231
4X-RAY DIFFRACTION4B38 - 125
5X-RAY DIFFRACTION5B126 - 156
6X-RAY DIFFRACTION6B157 - 231
7X-RAY DIFFRACTION7C38 - 125
8X-RAY DIFFRACTION8C126 - 156
9X-RAY DIFFRACTION9C157 - 231
10X-RAY DIFFRACTION10D38 - 125
11X-RAY DIFFRACTION11D126 - 156
12X-RAY DIFFRACTION12D157 - 231

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