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Yorodumi- PDB-5mhk: ICP4 DNA-binding domain in complex with 19mer DNA duplex from its... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mhk | ||||||
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Title | ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor / Herpes virus / Intercalation | ||||||
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) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 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 | 5mhk.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mhk.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mhk ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mhk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-DNA (5'-D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)- ... , 2 types, 4 molecules GEHF
#1: DNA chain | Mass: 5877.783 Da / Num. of mol.: 2 / 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) #2: DNA chain | Mass: 5775.739 Da / Num. of mol.: 2 / 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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-Protein / Protein/peptide , 2 types, 5 molecules ACDBJ
#3: Protein | Mass: 24398.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487 Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS LYSY / References: UniProt: Q09I77, UniProt: P08392*PLUS #4: Protein/peptide | | Mass: 394.422 Da / Num. of mol.: 1 Fragment: LIkely N-terminus of chain D, but chain connectivity is ambiguous Source method: isolated from a genetically manipulated source Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487 Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS LYSY / References: UniProt: Q09I77, UniProt: P08392*PLUS |
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-Non-polymers , 4 types, 245 molecules
#5: Chemical | ChemComp-MG / | ||||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / | #8: 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: 2.14 Å3/Da / Density % sol: 42.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Ammonium sulfate, 0.1 Bis/Tris pH 5.5 & 25% w/v PEG3350 [SG1 B8 Molecular Dimensions]. Cryoprotected with 20% PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→71.3 Å / Num. obs: 58110 / % possible obs: 99.92 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1613 / Net I/σ(I): 8.69 |
Reflection shell | Resolution: 2.28→2.362 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.333 / Mean I/σ(I) obs: 1.39 / CC1/2: 0.574 / % possible all: 99.95 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.28→71.3 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→71.3 Å
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Refine LS restraints |
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LS refinement shell |
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