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- PDB-7n10: Co-crystal structure of Prx with ComR DNA binding domain -

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Basic information

Entry
Database: PDB / ID: 7n10
TitleCo-crystal structure of Prx with ComR DNA binding domain
Components
  • ComR
  • Prx
KeywordsVIRAL PROTEIN/TRANSCRIPTION / paratox / ComR / Streptococcus / bacteriophage / quorum sensing / natural competence / VIRAL PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


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 / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Paratox / Putative transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
Streptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 26, 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
C: Prx


Theoretical massNumber of molelcules
Total (without water)23,7693
Polymers23,7693
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint5 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.556, 41.918, 90.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-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
Details: Cloning artifact
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 / Putative transcriptional regulator


Mass: 7578.767 Da / Num. of mol.: 1 / Fragment: DNA binding domain (UNP residues 1-66)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 1.53 Å3/Da / Density % sol: 19.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15 mg/mL protein, 20% PEG3500, 0.2 M potassium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.28329 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28329 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 18234 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 15.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 918 / CC1/2: 0.867 / Rpim(I) all: 0.316 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Cootmodel building
PHENIXphasing
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CKA
Resolution: 1.65→45 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 1819 5.38 %
Rwork0.175 31977 -
obs0.1763 18234 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 0 188 1239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421077
X-RAY DIFFRACTIONf_angle_d0.65521448
X-RAY DIFFRACTIONf_chiral_restr0.0461169
X-RAY DIFFRACTIONf_plane_restr0.0079182
X-RAY DIFFRACTIONf_dihedral_angle_d4.9092144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.38161120.35262517X-RAY DIFFRACTION99.81
1.69-1.740.31381630.2922476X-RAY DIFFRACTION99.77
1.74-1.80.25291320.22622419X-RAY DIFFRACTION99.65
1.8-1.870.22241490.21772441X-RAY DIFFRACTION99.62
1.87-1.940.2411210.21242481X-RAY DIFFRACTION98.9
1.94-2.030.23651390.21392473X-RAY DIFFRACTION99.92
2.03-2.130.2191980.17532488X-RAY DIFFRACTION99.65
2.14-2.270.23571260.16912476X-RAY DIFFRACTION99.46
2.27-2.440.19851410.16542439X-RAY DIFFRACTION99.54
2.44-2.690.19371880.16962413X-RAY DIFFRACTION99.85
2.69-3.080.1941470.16352444X-RAY DIFFRACTION99.69
3.08-3.880.17841500.15732464X-RAY DIFFRACTION99.51
3.88-450.15891530.15492446X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4830779865040.0705588714426-0.2226922565460.432965438456-0.2622152081510.232358202025-0.1298189383780.23415949559-0.186675043665-0.03388089259750.0957477441964-0.04507607012320.1481120297120.3454674095465.04458142586E-50.2845893759920.03851283673370.01104942122720.208065737585-0.0014136660940.24143099470114.4135474732-2.0213814769541.8703309899
20.991050617018-0.0712502272113-0.1747276055370.854657124971-0.3814345361650.622475991615-0.155541441134-0.0158034787944-0.07722377100080.04594239950760.2030983172790.114024895886-0.0870839914561-0.158386737980.005276294569140.1778777560120.004961781207970.005409862304460.1795628340430.02358894211960.1883965083878.695376804326.6638384514638.5858447212
30.749955653676-0.789052632753-0.2544495556761.016571957180.6230894166850.740726596803-0.1214982452840.0882208277212-0.09903440902440.2024584728580.1404121476630.164056154377-0.068994536987-0.1798438678811.17784586346E-50.191633990676-0.001380054009050.03064985491170.1925555840390.04178815773240.2455175050944.340493058124.2551832916139.1850190666
40.554753211506-0.206323366543-0.85057920021.207506088050.7534055781151.573650599570.0593009647549-0.04400610343760.00514867057241-0.01146482950570.0449609747749-0.2161975651970.07223810818810.0230265058979-0.000185676957480.2038959632860.0212511658513-0.005270632363910.251100493851-0.02053614140580.23894472814524.92793463164.0327624366126.9460751733
50.558828795323-0.323083354392-0.8103975252180.3331579536730.5780252041951.40728836695-0.0911202942927-0.0304824082368-0.0269021829939-0.01088556591640.0342971155654-0.07542170594230.1018766286790.0496986580881-6.3534225545E-60.2143656825240.01402301394680.009989084308720.215064161692-0.02129826023160.19542904349822.5800710685-0.30795564108329.1633909476
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 1:16)AA1 - 161 - 16
22(chain A and resid 17:39)AA17 - 3917 - 39
33(chain A and resid 40:60)AA40 - 6040 - 60
44(chain B and resid 1:30)BB1 - 301 - 30
55(chain B and resid 31:66)BB31 - 6631 - 66

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