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- PDB-8vsr: Co-crystal structure of Prx with Esub1 -

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Basic information

Entry
Database: PDB / ID: 8vsr
TitleCo-crystal structure of Prx with Esub1
Components
  • Esub1
  • Prx
KeywordsVIRAL PROTEIN / Bacteriophage / quorum sensing / Streptococcus pyogenes / paratox / protein binding / ComR
Function / homology
Function and homology information


DNA restriction-modification system / DNA binding
Similarity search - Function
Type I restriction-modification system, specificity subunit, predicted / : / : / Paratox / Type I restriction modification DNA specificity domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Type I restriction-modification system specificty subunit / Paratox
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS315 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsMuna, T.H. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: The phage protein paratox is a multifunctional metabolic regulator of Streptococcus.
Authors: Muna, T.H. / Rutbeek, N.R. / Horne, J. / Lao, Y.W. / Krokhin, O.V. / Prehna, G.
History
DepositionJan 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prx
B: Esub1
C: Prx
D: Esub1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7957
Polymers61,4994
Non-polymers2963
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.494, 67.494, 232.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Prx


Mass: 8095.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS315 (bacteria)
Gene: SpyM3_1300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UWN8
#2: Protein Esub1


Mass: 22654.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS315 (bacteria)
Gene: SpyM3_0890
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H2UUU0
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 50% PEG 200, 200mM sodium chloride, 100mM sodium/potassium phosphate pH 6.2, 12mg/mL protein

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Data collection

DiffractionMean temperature: 108.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→38.7 Å / Num. obs: 16490 / % possible obs: 99.47 % / Redundancy: 10.8 % / Biso Wilson estimate: 52.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.045 / Net I/σ(I): 13.3
Reflection shellResolution: 2.69→2.786 Å / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2073 / CC1/2: 0.652 / Rsym value: 0.308 / % possible all: 95.82

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→38.7 Å / SU ML: 0.3722 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.5581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2654 827 5.02 %
Rwork0.2279 15661 -
obs0.2298 16488 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.28 Å2
Refinement stepCycle: LAST / Resolution: 2.69→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 17 123 4088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284024
X-RAY DIFFRACTIONf_angle_d0.52945426
X-RAY DIFFRACTIONf_chiral_restr0.0444624
X-RAY DIFFRACTIONf_plane_restr0.0044687
X-RAY DIFFRACTIONf_dihedral_angle_d15.55011538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.850.38821310.30862496X-RAY DIFFRACTION95.28
2.85-3.080.32341440.27482640X-RAY DIFFRACTION100
3.08-3.380.28171460.26392618X-RAY DIFFRACTION100
3.38-3.870.30981110.23132655X-RAY DIFFRACTION99.96
3.87-4.880.21241500.19342622X-RAY DIFFRACTION100
4.88-38.70.24681450.20742630X-RAY DIFFRACTION99.64
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)
14.33511041627-0.956128157829-3.660810279963.43714956589-0.7586923363813.881307740181.22525367456-0.5652301116740.2716554595080.892284393624-0.191086770203-1.20048160467-0.0192304990060.945159108697-0.580217090850.6417374857530.0666944253877-0.3000226664390.502574617561-0.1339931966470.610229597546-23.1351201496-18.2553909123-18.3796394814
22.5416644819-0.6193275566661.508847132658.519302369230.8574859697474.755466964750.23401905020.405791069022-0.4591256800220.04547019427410.222975878214-0.2146888660810.1395281602340.158633745433-0.3340828788890.5291197479450.130513039106-0.14665852140.523836217781-0.1175374391710.488652465663-18.6366672627-21.1643687962-27.5647118392
35.307493959650.739294386069-0.4157842484216.07976396659-1.01409699925.33088427511-0.0386951039346-1.131239497170.8318505569190.522208762431-0.02265114865180.1722693060350.520519448797-0.166517141384-0.02857263020090.411186545776-0.117462017687-0.008635519884290.423506116337-0.1368361547930.52734225419-35.0274488433-4.53268721473-7.2838762355
43.546031204123.057831360761.581301069912.776091618940.8435409295862.309686230130.921524637389-0.903644516228-1.956271742150.000666441291963-0.652812827103-1.917393285530.9431655175543.22910777120.8810579902580.6789090054630.05662358027870.07166496072391.224318914830.1148916344460.84822499296-8.01437453507-5.98614539673-20.2552894457
56.884227816640.8464073521992.296110481945.04106353139-4.085039935945.35767913321-0.212063516809-0.9991185175680.05655331697230.642269452877-0.342460120091-0.235614563049-0.2537392826470.7917317658430.3136575800550.3982554524980.0371248174322-0.1133683853910.389356205452-0.09815351515280.63948779317-12.49670258143.79850551467-12.2946794414
62.480457189070.379185319226-0.396544801143.416129074950.8482985547043.519878460170.0842191796284-0.253984878409-0.009227349067630.0314671035716-0.320683950885-0.06752216898150.32305481220.3647403523360.08181443140140.3411829371090.0652251857554-0.01133540517240.4051015315290.07138923148820.65013037049-19.6740812562-3.62826166423-16.028119115
74.936211152211.343841029440.2944081775913.835554794030.8055190050622.234649531170.226970376918-0.6040332506630.3853590150870.459115600819-0.231264122841-0.1846870363450.225992987450.0489273616450.1490576292370.36447420657-0.0179590983076-0.113968889610.300522921961-0.05117414610410.212897827815-26.00987868331.66595755326-8.13935041505
80.08125027245930.1782164846060.05706320837035.349404961031.332432574340.3351912380110.301978811306-1.86852329932-0.4770672638781.3625776320.0887786973227-0.5451376545870.3056346275070.346095654046-0.1384359488480.70675344768-0.304154155143-0.2136329791021.01126588530.2120618067110.842672939002-19.1686263343-11.77690260452.20538119638
92.598288580762.898354472161.928648999061.568666786671.068783189011.74766956875-0.516424562029-0.2477482252880.556253526016-0.227496769079-0.06234674967970.190702724928-0.3272997837130.04003745864540.5496451626240.358742717827-0.0342719882369-0.09464829756910.466709585462-0.08992212593440.566653365154-20.321675964717.1523177536-4.21827638035
107.481740729893.2743378134-0.5103498361148.33305888936-0.3452517011992.812692363850.8967401290391.351745865210.296869711689-0.4681932121510.5902462221651.280731554091.435239256290.796797819049-0.8956352842250.5973496910650.155580728261-0.1748696040040.6509772095650.08202215087080.49063451246124.99240451218.3839232094418.7024227091
113.92021115603-1.117063353490.9246497408385.9935288674-1.376562311125.968517776630.505172384173-0.284212540443-1.061016776710.54307459499-0.0453996558343-0.03563063014630.190738067778-0.257742751289-0.4884472152320.4677061746440.0437590498331-0.147422781380.3336318552460.05770937968670.63313782458325.85404673249.0182440365730.1598236379
126.3305391935-3.13993767659-1.541490912117.91139001048-0.6939335307965.356692680440.7184681371131.38687673015-0.8017326139310.0792243571892-0.9861564959710.1432695147721.38512736489-0.251030874728-0.04872902778990.7836542474810.35482124659-0.2481150108560.651485853005-0.01341371065720.42279486606332.9751171522.5206727937923.9747608
135.525291659121.580867676370.4179100513223.866536238631.486885698823.70680412006-0.260455421840.290446019363-0.319999421411-0.4997152099010.3917247564650.6442949199570.836986470601-0.487611177555-0.1191207197850.439082213465-0.0130492760873-0.07535208721060.3074566737620.01934924477720.498054597969.890674415915.496470392814.0347367872
144.505836737540.6650931746650.380649739052.18891402267-0.9156509039161.6742878539-0.05841389256360.357852788446-0.103361094609-0.2675855320260.2788393638880.3202726345710.2927789835130.0611967262872-0.2022721781540.293334383251-0.0204270187975-0.01016234131420.361694383631-0.02264079871220.37600961408413.026772151319.128447547211.0359277455
156.100067511181.44678165052.36993161362-0.06352142611051.293693594591.5556636559-0.07218464444660.2038830090360.7618929359190.00757861986643-0.1924928225930.351521648536-0.0834526986521-0.2219794044140.346915655120.374498404244-0.0577888179317-0.07477630460440.436259822526-0.03359447905340.594077720855-4.1534057978226.47284683125.78112978752
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 19 )AA1 - 191 - 19
22chain 'A' and (resid 20 through 60 )AA20 - 6020 - 60
33chain 'B' and (resid 13 through 26 )BC13 - 261 - 14
44chain 'B' and (resid 27 through 38 )BC27 - 3815 - 26
55chain 'B' and (resid 39 through 60 )BC39 - 6027 - 48
66chain 'B' and (resid 61 through 87 )BC61 - 8749 - 75
77chain 'B' and (resid 88 through 133 )BC88 - 13376 - 121
88chain 'B' and (resid 134 through 144 )BC134 - 144122 - 132
99chain 'B' and (resid 145 through 197 )BC145 - 197133 - 185
1010chain 'C' and (resid 1 through 12 )CD1 - 121 - 12
1111chain 'C' and (resid 13 through 45 )CD13 - 4513 - 45
1212chain 'C' and (resid 46 through 60 )CD46 - 6046 - 60
1313chain 'D' and (resid 13 through 60 )DE13 - 601 - 48
1414chain 'D' and (resid 61 through 144 )DE61 - 14449 - 132
1515chain 'D' and (resid 145 through 196 )DE145 - 196133 - 184

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