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Yorodumi- PDB-8qao: Crystal structure of TP901-1 CI-NTD89 repressor N-terminal domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qao | ||||||
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Title | Crystal structure of TP901-1 CI-NTD89 repressor N-terminal domain | ||||||
Components | CI | ||||||
Keywords | DNA BINDING PROTEIN / repressor / DNA binding / genetic switch / temperate bacteriophage | ||||||
Function / homology | latency-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 species | Lactococcus phage TP901-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Huang, Z. / Hamad, G.M. / Lo Leggio, L. / Varming, A.K. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qao.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qao.ent.gz | 41 KB | Display | PDB format |
PDBx/mmJSON format | 8qao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qao_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 8qao_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 8qao_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 8qao_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/8qao ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qao | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 28% w/v PEG 4000, 0.17 M ammonium sulphate and 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.29→1.37 Å / Num. unique obs: 5596 / CC1/2: 0.217 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.281 Å2
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Refinement step | Cycle: 1 / Resolution: 1.29→42.27 Å
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Refine LS restraints |
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