[English] 日本語
![](img/lk-miru.gif)
- PDB-5mhk: ICP4 DNA-binding domain in complex with 19mer DNA duplex from its... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mhk | ||||||
---|---|---|---|---|---|---|---|
Title | ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter | ||||||
![]() |
| ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() DNA-templated viral transcription / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 201.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 156.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() Plasmid: PET-21A / Production host: ![]() ![]() ![]() #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.) ![]() ![]() ![]() Plasmid: PET-21A / Production host: ![]() ![]() ![]() |
---|
-Non-polymers , 4 types, 245 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / | ||||
---|---|---|---|---|---|
#6: Chemical | ChemComp-SO4 / ![]() #7: Chemical | ChemComp-CL / | ![]() #8: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.57 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→71.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|