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- PDB-6cka: Crystal Structure of Paratox -

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Basic information

Entry
Database: PDB / ID: 6cka
TitleCrystal Structure of Paratox
ComponentsParatox
KeywordsVIRAL PROTEIN / prophage / natural competence / Streptococcus / protein binding
Function / homologyParatox
Function and homology information
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.559 Å
AuthorsPrehna, G.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091779 United States
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: Sci Rep / Year: 2018
Title: The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus.
Authors: Mashburn-Warren, L. / Goodman, S.D. / Federle, M.J. / Prehna, G.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.grant_number
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paratox
B: Paratox


Theoretical massNumber of molelcules
Total (without water)16,3782
Polymers16,3782
Non-polymers00
Water3,603200
1
A: Paratox


Theoretical massNumber of molelcules
Total (without water)8,1891
Polymers8,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Paratox


Theoretical massNumber of molelcules
Total (without water)8,1891
Polymers8,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.689, 56.816, 88.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Paratox


Mass: 8189.015 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria)
Strain: ATCC BAA-595 / MGAS315 / Gene: SpyM3_1300 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UWN8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1:1 13-26 mg/mL Paratox with 30% PEG4000, 0.1 M ammonium acetate, 0.1 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979498 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979498 Å / Relative weight: 1
ReflectionResolution: 1.559→50 Å / Num. obs: 19842 / % possible obs: 99.2 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rrim(I) all: 0.114 / Net I/σ(I): 11.6
Reflection shellResolution: 1.559→1.65 Å / Num. unique obs: 3119 / CC1/2: 0.682 / Rrim(I) all: 0.616

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
PHENIXphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.559→47.791 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.42
RfactorNum. reflection% reflection
Rfree0.1835 1007 5.1 %
Rwork0.1623 --
obs0.1635 19759 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.559→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 0 200 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081187
X-RAY DIFFRACTIONf_angle_d0.8851606
X-RAY DIFFRACTIONf_dihedral_angle_d12.964716
X-RAY DIFFRACTIONf_chiral_restr0.064178
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5591-1.64130.21411320.20532594X-RAY DIFFRACTION98
1.6413-1.74420.19621420.18792614X-RAY DIFFRACTION99
1.7442-1.87880.22891500.18262629X-RAY DIFFRACTION99
1.8788-2.06790.20731540.16432632X-RAY DIFFRACTION99
2.0679-2.36710.19061480.15132679X-RAY DIFFRACTION100
2.3671-2.98230.17251440.16772738X-RAY DIFFRACTION100
2.9823-4.670.16331370.14992866X-RAY DIFFRACTION100
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)
16.77274.25593.93476.0365-2.07551.99230.16570.9748-0.9758-0.65610.4991-0.93721.47670.7594-0.02550.27620.00750.05840.2492-0.0760.15955.26427.85769.4705
27.7501-1.1779-2.77865.10063.15247.63250.01690.25350.1561-0.24950.11150.1203-0.1813-0.242-0.10130.1071-0.0054-0.0090.10040.02260.1215-2.723915.210716.2682
34.2208-3.3286-2.62425.39054.25236.39710.14940.079-0.0035-0.1617-0.1699-0.66220.00650.1674-0.01520.11310.02350.03690.09220.00940.15268.76578.372820.0605
44.9239-0.1267-1.9552.4008-0.4514.9674-0.0143-0.11820.036-0.13670.00490.07730.1116-0.07740.00510.1205-0.0052-0.00750.0859-0.01380.13232.01415.803521.9119
56.5676-5.432-4.28595.70143.01448.54140.24420.3699-0.3497-0.08140.0276-0.59840.2119-0.2933-0.1050.1825-0.011-0.01180.07710.01050.29316.3006-3.835424.7351
63.9347-0.95881.13941.9375-3.23425.6414-0.04670.1075-0.10820.05590.0031-0.1732-0.00980.25420.04340.0808-0.0155-0.00670.0822-0.00450.122310.86510.570423.4544
76.25086.18124.42246.85654.64813.7681-0.3297-0.2321-0.0451-0.4661-0.14580.2779-1.0740.67330.27520.1826-0.0321-0.0210.18520.04870.09879.532516.080613.9614
80.27140.4609-0.46214.4929-4.74074.70960.0864-0.09990.02340.64010.16550.1996-0.9451-0.2684-0.28440.204-0.01890.03330.1870.01850.11879.819316.6023-2.3112
96.34995.7029-0.86245.5425-0.06212.35590.3144-0.7277-1.13770.321-0.3732-0.64960.24030.18840.15040.1917-0.051-0.02230.21750.0590.249211.713915.339245.9183
109.24653.8706-0.70915.7138-3.95373.41410.0138-0.07290.3463-0.0402-0.0594-0.1587-0.02790.13530.06880.1787-0.0250.02970.1204-0.00830.158314.984822.263737.5822
115.42023.6281-3.01013.1761-1.19752.59550.17320.75260.5189-0.0631-0.12630.1385-1.06750.0132-0.14190.2639-0.0057-0.01670.17380.0350.20526.948621.821930.1769
126.62260.7647-2.52175.0554-2.16976.94570.0548-0.4388-0.24850.4141-0.16020.26270.2769-0.0950.15040.1519-0.04920.0170.1213-0.01020.11096.816610.117238.8498
137.8596.2776-4.37096.593-6.17957.4922-0.0736-0.0004-0.55550.24430.0206-0.41630.16310.00020.17320.14690.01220.00560.12850.00230.147213.55796.408429.6019
143.42640.6073-0.25328.75223.13444.4880.1583-0.0486-0.0146-0.3532-0.37450.364-0.0731-0.36020.2030.1261-0.0152-0.00130.1509-0.02520.1242.847113.130634.0259
156.9877-2.8532-1.51134.3956-2.83564.14450.13110.0220.6031-0.0152-0.2681-0.1536-0.1488-0.32460.07820.1997-0.00270.02070.1622-0.04570.16982.453920.955841.5578
161.0569-2.4028-2.79915.53146.50336.83920.10820.1445-0.0025-0.41620.0399-0.1376-0.71590.346-0.39650.2007-0.02950.03850.1916-0.02810.15733.426423.267656.4366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:4)
2X-RAY DIFFRACTION2(chain A and resid 5:16)
3X-RAY DIFFRACTION3(chain A and resid 17:29)
4X-RAY DIFFRACTION4(chain A and resid 30:38)
5X-RAY DIFFRACTION5(chain A and resid 39:44)
6X-RAY DIFFRACTION6(chain A and resid 45:51)
7X-RAY DIFFRACTION7(chain A and resid 52:59)
8X-RAY DIFFRACTION8(chain A and resid 60:68)
9X-RAY DIFFRACTION9(chain B and resid 1:5)
10X-RAY DIFFRACTION10(chain B and resid 6:16)
11X-RAY DIFFRACTION11(chain B and resid 17:21)
12X-RAY DIFFRACTION12(chain B and resid 22:35)
13X-RAY DIFFRACTION13(chain B and resid 36:42)
14X-RAY DIFFRACTION14(chain B and resid 43:52)
15X-RAY DIFFRACTION15(chain B and resid 53:57)
16X-RAY DIFFRACTION16(chain B and resid 58:68)

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