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- PDB-6tri: CI-MOR repressor-antirepressor complex of the temperate bacteriop... -

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Basic information

Entry
Database: PDB / ID: 6tri
TitleCI-MOR repressor-antirepressor complex of the temperate bacteriophage TP901-1 from Lactococcus lactis
Components
  • CI
  • MOR
KeywordsVIRAL PROTEIN / Complex / regulation / DNA-binding / temperate virus
Function / homology
Function and homology information


latency-replication decision / DNA binding
Similarity search - Function
Protein of unknown function DUF739 / Protein of unknown function (DUF739) / 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
Similarity search - Domain/homology
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.277 Å
AuthorsRasmussen, K.K. / Blackledge, M. / Herrmann, T. / Jensen, M.R. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4002-00107 Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Revealing the mechanism of repressor inactivation during switching of a temperate bacteriophage.
Authors: Rasmussen, K.K. / Palencia, A. / Varming, A.K. / El-Wali, H. / Boeri Erba, E. / Blackledge, M. / Hammer, K. / Herrmann, T. / Kilstrup, M. / Lo Leggio, L. / Jensen, M.R.
History
DepositionDec 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CI
B: MOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5624
Polymers19,3702
Non-polymers1922
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, information from mass spectrometry, NMR, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-33 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.405, 94.405, 30.558
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-101-

SO4

21B-210-

HOH

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Components

#1: Protein CI


Mass: 10947.503 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: cI / Production host: Escherichia coli (E. coli) / References: UniProt: O48503
#2: Protein MOR


Mass: 8422.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: mor / Production host: Escherichia coli (E. coli) / References: UniProt: O48504
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350 in reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.277→42.7 Å / Num. obs: 7285 / % possible obs: 99.9 % / Redundancy: 16.1 % / CC1/2: 0.996 / Net I/σ(I): 7.95
Reflection shellResolution: 2.277→2.41 Å / Num. unique obs: 1184 / CC1/2: 0.377

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A7L + MOR NMR structure (just deposited 6TO6)

5a7l

6to6


Resolution: 2.277→40.879 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.3
RfactorNum. reflection% reflection
Rfree0.2174 365 5.01 %
Rwork0.1889 --
obs0.1904 7282 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.6 Å2 / Biso mean: 58.2949 Å2 / Biso min: 29.95 Å2
Refinement stepCycle: final / Resolution: 2.277→40.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 10 20 1224
Biso mean--83.2 59.44 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021222
X-RAY DIFFRACTIONf_angle_d0.6421648
X-RAY DIFFRACTIONf_chiral_restr0.021188
X-RAY DIFFRACTIONf_plane_restr0.004204
X-RAY DIFFRACTIONf_dihedral_angle_d10.799460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRefine-ID
2.277-2.60.326117X-RAY DIFFRACTION
2.6-3.280.3171122X-RAY DIFFRACTION
3.28-40.870.1655126X-RAY DIFFRACTION
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)
17.05640.97521.12696.144-0.26189.5254-0.01760.07390.1541-0.0534-0.0032-0.0442-0.31130.3060.05470.22720.00230.01840.3120.00320.387510.358541.72556.0448
28.1192-1.4693-0.84135.0523-1.15336.08-0.0197-0.0727-0.24580.01440.0866-0.0616-0.00380.1871-0.10.2815-0.06890.00550.25270.00460.3611-5.792731.234414.872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 80
2X-RAY DIFFRACTION2chain BB2 - 70

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