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- PDB-8qao: Crystal structure of TP901-1 CI-NTD89 repressor N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8qao
TitleCrystal structure of TP901-1 CI-NTD89 repressor N-terminal domain
ComponentsCI
KeywordsDNA BINDING PROTEIN / repressor / DNA binding / genetic switch / temperate bacteriophage
Function / homologylatency-replication decision / 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 / DNA binding / CI
Function and homology information
Biological speciesLactococcus phage TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsHuang, Z. / Hamad, G.M. / Lo Leggio, L. / Varming, A.K.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Microbiome Res Rep / Year: 2024
Title: CI:Mor interactions in the lysogeny switches of Lactococcus lactis TP901-1 and Staphylococcus aureus phi 13 bacteriophages.
Authors: Varming, A.K. / Huang, Z. / Hamad, G.M. / Rasmussen, K.K. / Ingmer, H. / Kilstrup, M. / Lo Leggio, L.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CI


Theoretical massNumber of molelcules
Total (without water)10,9481
Polymers10,9481
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.369, 48.369, 86.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-206-

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 BL21(DE3) (bacteria) / References: UniProt: O48503
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 28% w/v PEG 4000, 0.17 M ammonium sulphate and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.29→43.48 Å / Num. obs: 46858 / % possible obs: 94 % / Redundancy: 19.04 % / CC1/2: 0.99 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.051 / Net I/σ(I): 18.5
Reflection shellResolution: 1.29→1.37 Å / Num. unique obs: 5596 / CC1/2: 0.217

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.29→42.27 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.074 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18288 1134 4.5 %RANDOM
Rwork0.14969 ---
obs0.15111 46858 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.281 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å2-0 Å2
2--0.98 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.29→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 0 107 769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.013798
X-RAY DIFFRACTIONr_bond_other_d0.0030.016810
X-RAY DIFFRACTIONr_angle_refined_deg2.2961.6311089
X-RAY DIFFRACTIONr_angle_other_deg1.5741.5851891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2045110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24924.70634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58715173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.041153
X-RAY DIFFRACTIONr_chiral_restr0.1120.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02917
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02173
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.111.311395
X-RAY DIFFRACTIONr_mcbond_other1.9461.295394
X-RAY DIFFRACTIONr_mcangle_it2.2781.954506
X-RAY DIFFRACTIONr_mcangle_other2.3961.964507
X-RAY DIFFRACTIONr_scbond_it4.3481.883403
X-RAY DIFFRACTIONr_scbond_other4.3431.886404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3662.58578
X-RAY DIFFRACTIONr_long_range_B_refined5.34818.966927
X-RAY DIFFRACTIONr_long_range_B_other4.81817.727904
X-RAY DIFFRACTIONr_rigid_bond_restr8.78631608
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.294→1.327 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.657 54 -
Rwork0.616 1115 -
obs--61.2 %

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