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Yorodumi- PDB-5mhj: ICP4 DNA-binding domain, lacking intrinsically disordered region,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mhj | ||||||
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Title | ICP4 DNA-binding domain, lacking intrinsically disordered region, in complex with 12mer DNA duplex from its own promoter | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor / Dimer / Herpes / Virus | ||||||
Function / homology | Function and homology information DNA-templated viral transcription / viral tegument / response to type I interferon / host cell cytoplasm / host cell nucleus / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 Å | ||||||
Authors | Tunnicliffe, R.B. / Lockhart-Cairns, M.P. / Levy, C. / Mould, P. / Jowitt, T.A. / Sito, H. / Baldock, C. / Sandri-Goldin, R.M. / Golovanov, A.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: The herpes viral transcription factor ICP4 forms a novel DNA recognition complex. Authors: Tunnicliffe, R.B. / Lockhart-Cairns, M.P. / Levy, C. / Mould, A.P. / Jowitt, T.A. / Sito, H. / Baldock, C. / Sandri-Goldin, R.M. / Golovanov, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mhj.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mhj.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 5mhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mhj_validation.pdf.gz | 463.2 KB | Display | wwPDB validaton report |
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Full document | 5mhj_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 5mhj_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5mhj_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mhj ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mhj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21311.943 Da / Num. of mol.: 2 / Fragment: DNA binding domain, UNP residues 288-487 Source method: isolated from a genetically manipulated source Details: DNA binding domain of ICP4, residues 288-487 / Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: ICP4, IE175, RS1 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Variant (production host): T7 express LysY / References: UniProt: P08392 |
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-DNA (5'-D(P*CP*GP*AP*TP*CP*GP*TP*CP*C)- ... , 2 types, 2 molecules EF
#2: DNA chain | Mass: 3583.344 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic DNA, sequences matches a region from the ICP4 promoter (IE3) Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1) |
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#3: DNA chain | Mass: 3743.440 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic DNA, sequences matches a region from the ICP4 promoter (IE3) Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1) |
-Non-polymers , 3 types, 199 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium HEPES, pH 7.5, 25% w/v PEG 3350 [SG1 HT96 F2 Molecular Dimensions] cryoprotected with Perfluoropolyether Cryo Oil |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.117→45.22 Å / Num. obs: 25175 / % possible obs: 94.77 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1156 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 2.117→2.193 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7708 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.847 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ICP4N-19mer complex Resolution: 2.117→45.22 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.117→45.22 Å
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Refine LS restraints |
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LS refinement shell |
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