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- PDB-7n1n: Prx in complex with ComR DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 7n1n
TitlePrx in complex with ComR DNA-binding domain
Components
  • ComR
  • Prx
KeywordsVIRAL PROTEIN/TRANSCRIPTION / Paratox / bacteriophage / quorum sensing / Streptococcus / ComR / natural competence / VIRAL PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


: / Paratox / ComR, tetratricopeptide / ComR tetratricopeptide / : / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain ...: / Paratox / ComR, tetratricopeptide / ComR tetratricopeptide / : / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Paratox / Transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
Streptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRutbeek, N.R. / Prehna, G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04968 Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular mechanism of quorum sensing inhibition in Streptococcus by the phage protein paratox.
Authors: Rutbeek, N.R. / Rezasoltani, H. / Patel, T.R. / Khajehpour, M. / Prehna, G.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prx
B: ComR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8163
Polymers15,5782
Non-polymers2381
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint11 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.814, 36.814, 189.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Prx


Mass: 8095.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315) (bacteria)
Strain: ATCC BAA-595 / MGAS315 / Gene: SpyM3_1300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UWN8
#2: Protein ComR / transcriptional regulator


Mass: 7482.656 Da / Num. of mol.: 1 / Fragment: DNA-binding domain (UNP residues 1-68)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: SMU_61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DWI6
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: 10 mg/mL protein, 0.1 M HEPES, pH 7.0, 18% PEG12000, 50 ug/mL chymotrypsin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.6→47.32 Å / Num. obs: 18256 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1746 / CC1/2: 0.641 / Rpim(I) all: 0.46 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Cootmodel building
XDSdata scaling
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CKA

6cka


Resolution: 1.6→47.32 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2039 909 4.98 %
Rwork0.179 17346 -
obs0.1803 18255 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.71 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 15 206 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491121
X-RAY DIFFRACTIONf_angle_d0.68121505
X-RAY DIFFRACTIONf_chiral_restr0.0471172
X-RAY DIFFRACTIONf_plane_restr0.008187
X-RAY DIFFRACTIONf_dihedral_angle_d12.9447433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.29441260.25242784X-RAY DIFFRACTION99.79
1.7-1.830.23161380.21082852X-RAY DIFFRACTION99.97
1.83-2.020.22071720.18772812X-RAY DIFFRACTION100
2.02-2.310.17261580.16662865X-RAY DIFFRACTION100
2.31-2.910.19241540.17272903X-RAY DIFFRACTION100
2.91-47.320.2041610.17143130X-RAY DIFFRACTION99.97
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)
10.420123508770.2763788767410.5667828546391.733765266960.4125682197821.42931131971-0.0311899815946-0.007900489582720.00893001020118-0.1042981261330.0609267058646-0.05747614290430.1193779790570.034653363299-0.03300005620760.179060426350.006138938853210.01171249060150.1329784998710.002098345993880.14407633834-6.464323494-19.6274266372-6.96056214423
22.6423304221.177499696980.5563268008692.363713609281.681799312525.22156455475-0.1338572425860.001921227556930.0546609941689-0.2264902498710.2940429051960.201990006108-0.189595904469-0.122927552523-0.0703508518140.322462184123-0.0511427755494-0.08432424970690.2431980249270.05601826986740.237184896428-16.6555351937-22.1840269109-16.7015525855
34.96794348796-0.0388794979592-0.6528861221552.010907039780.240960200942.84100701151-0.150643207423-0.274701814533-0.3086455617180.173091317750.125971585108-0.1610657747420.4691083367340.300207698755-0.02728272654820.2738908119990.0460444686852-0.007701353354570.2012508154930.004012301135060.21212276098-1.1534417829-27.2113512171-5.20349812846
43.01364622282-0.754238212395-0.1769210254253.483661898111.205315917782.253989065360.248135695959-0.718313290510.188626310261-0.14324622457-0.03453084248940.494252166956-0.118046624064-0.367696206636-0.1050152827340.4479776506780.05041375418520.02835323943640.569280849739-0.07353177436870.43602538831415.9887627382-28.2308534359-17.0518447633
52.22445341734-0.594139012262-0.9756426039452.30638903823-0.03340486638640.498104849077-0.0975928613766-0.355942118139-0.02596138003130.3166046079980.0484489633228-0.273821823013-0.134318407598-0.0175547057849-0.008037458896550.2218989349670.00382010097273-0.0005144273830560.131805056724-0.006504566306560.201000195062-4.141810283450.318075185678-13.0291938835
61.13673225766-0.897744387323-0.01335266632532.13378079483-0.3473881807231.01200326916-0.0332769812789-0.0573149705581-0.0565803671488-0.1873278154730.0776450005337-0.02812167953360.0613544152506-0.028898489495-0.04907509116490.233392487586-0.0100350104927-0.01037929082870.153607587541-0.005785192833880.170344370384-10.1852754488-7.66946164338-21.845782322
71.14516431321-0.474168160072-0.4655506645630.956410910577-0.4201324281371.12037463890.0653483632780.01368921151390.094238052949-0.164856168368-0.02069765751690.02034101236090.05649918507770.0626560278533-0.01879275720440.1872511232620.002742810357580.002308920765770.119138960014-0.001000601842350.139163038125-3.47052096361-6.50314448049-16.2430589844
82.00040957083-4.268866087513.711448094341.80775127076-1.377816425012.506905542080.1135770246610.5773364636881.01430062557-0.870469290361-0.2489498265280.480661699579-0.615393393468-0.2533872497010.03054722494590.8967715665280.037720745745-0.02010897833980.355376750699-0.09555712921380.5896169515967.267478481464.44882684327-14.6682995911
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 1:38)AA1 - 381 - 38
22(chain A and resid 39:46)AA39 - 4639 - 46
33(chain A and resid 47:62)AA47 - 6247 - 62
44(chain A and resid 63:68)AA63 - 6863 - 68
55(chain B and resid 1:13)BC1 - 131 - 13
66(chain B and resid 14:30)BC14 - 3014 - 30
77(chain B and resid 31:64)BC31 - 6431 - 64
88(chain B and resid 65:68)BC65 - 6865 - 68

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