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Yorodumi- PDB-5jlt: The crystal structure of the bacteriophage T4 MotA C-terminal dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jlt | ||||||
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Title | The crystal structure of the bacteriophage T4 MotA C-terminal domain in complex with dsDNA reveals a novel protein-DNA recognition motif | ||||||
Components |
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Keywords | VIRAL PROTEIN/DNA / MotA / dsDNA / "Double wing" / DNA binding motif / VIRAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å | ||||||
Authors | Cuypers, M.G. / Robertson, R.M. / Knipling, L. / Hinton, D.M. / White, S.W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA. Authors: Cuypers, M.G. / Robertson, R.M. / Knipling, L. / Waddell, M.B. / Moon, K. / Hinton, D.M. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jlt.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jlt.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jlt_validation.pdf.gz | 483.8 KB | Display | wwPDB validaton report |
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Full document | 5jlt_full_validation.pdf.gz | 504.3 KB | Display | |
Data in XML | 5jlt_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 5jlt_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/5jlt ftp://data.pdbj.org/pub/pdb/validation_reports/jl/5jlt | HTTPS FTP |
-Related structure data
Related structure data | 1kafS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 14548.928 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: non-native amino acids from expression vector= EGDIHM. N-TERM RESIDUES (93-96) = ELLK. LINKER (97-104) = KRATRKAR. HTTP://WWW.UNIPROT.ORG/UNIPROT/P22915 Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: motA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22915 #2: DNA chain | Mass: 6710.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 6790.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 23% PEG 8K, 0.1 M Na Acetate, 0.1 M NaCacodylate, pH 6.5, and 3% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.955→93.12 Å / Num. obs: 17332 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.167 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.955→3.11 Å / Redundancy: 23.5 % / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KAF + DNA helix from COOT Resolution: 2.955→62.588 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 35.46 Details: The settings of PHENIX.REFINE were tuned to use reference model restraints (PDB: 1KAF), NCS and the twin law K,H,-L.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.955→62.588 Å
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Refine LS restraints |
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LS refinement shell |
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