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- PDB-3qb2: The Crystal Structure of Immunity Factor for SPN (IFS) -

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Basic information

Entry
Database: PDB / ID: 3qb2
TitleThe Crystal Structure of Immunity Factor for SPN (IFS)
ComponentsImmunity factor for SPN
KeywordsHYDROLASE INHIBITOR / Glycohydrolase Inhibitor / Streptococcus pyogenes glycohydrolase toxin
Function / homologySerine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #520 / Immunity factor for SPN / IFS superfamily / Immunity factor for SPN / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Immunity factor for SPN
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSmith, C.L. / Ellenberger, T.
CitationJournal: Structure / Year: 2011
Title: Structural Basis of Streptococcus pyogenes Immunity to Its NAD(+) Glycohydrolase Toxin.
Authors: Smith, C.L. / Ghosh, J. / Elam, J.S. / Pinkner, J.S. / Hultgren, S.J. / Caparon, M.G. / Ellenberger, T.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunity factor for SPN
B: Immunity factor for SPN
C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,03710
Polymers89,4604
Non-polymers5766
Water2,792155
1
A: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6534
Polymers22,3651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4612
Polymers22,3651
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Immunity factor for SPN
B: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1146
Polymers44,7302
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-66 kcal/mol
Surface area16370 Å2
MethodPISA
6
C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9224
Polymers44,7302
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-46 kcal/mol
Surface area17040 Å2
MethodPISA
7
A: Immunity factor for SPN
B: Immunity factor for SPN
hetero molecules

C: Immunity factor for SPN
D: Immunity factor for SPN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,03710
Polymers89,4604
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area10970 Å2
ΔGint-147 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.032, 108.032, 147.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Immunity factor for SPN / SPN immunity factor


Mass: 22365.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ifs / Production host: Escherichia coli (E. coli) / References: UniProt: Q2VJ58
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT THE C-TERMINAL 26 RESIDUES ARE MADE OF LINKER (FRSFL), MOUSE C-MYC (EQKLISEEDL), ...AUTHOR STATES THAT THE C-TERMINAL 26 RESIDUES ARE MADE OF LINKER (FRSFL), MOUSE C-MYC (EQKLISEEDL), LINKER (NSAVD) AND 6XHIS TAGS

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6-2.0 ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97901, 0.97932, 0.99504
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 1, 2005
Details: Rosenbaum-Rock Si(111) sagitally focused monochromator
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979321
30.995041
ReflectionResolution: 2.5→46.8 Å / Num. obs: 34514 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.24 % / Rsym value: 0.069

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
REFMAC5.5.0070refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→46.78 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.862 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28986 1739 5 %RANDOM
Rwork0.25875 ---
all0.26042 66456 --
obs0.26042 32775 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 30 155 5085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225032
X-RAY DIFFRACTIONr_bond_other_d0.0010.023104
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.9686852
X-RAY DIFFRACTIONr_angle_other_deg0.87337595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0655647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23824.654217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.215750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0661515
X-RAY DIFFRACTIONr_chiral_restr0.0660.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5251.53242
X-RAY DIFFRACTIONr_mcbond_other0.0741.51310
X-RAY DIFFRACTIONr_mcangle_it1.03125094
X-RAY DIFFRACTIONr_scbond_it1.6931790
X-RAY DIFFRACTIONr_scangle_it2.6734.51758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 151 -
Rwork0.372 2407 -
obs--99.92 %

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