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- PDB-8kfu: Crystal structure of ZmMOC1 in complex with a nicked Holliday jun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kfu | ||||||
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Title | Crystal structure of ZmMOC1 in complex with a nicked Holliday junction soaked in Mn2+ for 180 seconds | ||||||
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![]() | HYDROLASE / MOC1 / Holliday junction / Time-resolved crystallography | ||||||
Function / homology | Holliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / : / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, D. / Luo, Z. / Lin, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions. Authors: Zhang, D. / Xu, S. / Luo, Z. / Lin, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.4 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kfrC ![]() 8kfsC ![]() 8kftC ![]() 8kfvC ![]() 8kfwC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17616.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 3 types, 3 molecules CDE
#2: DNA chain | Mass: 10137.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#3: DNA chain | Mass: 7665.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 3 types, 205 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MN / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: 6% Isopropyl alcohol, 0.1 M Sodium acetate pH5.0, 35% Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 23115 / % possible obs: 96.5 % / Redundancy: 4.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.0903 / Net I/σ(I): 3.04 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.4078 / Mean I/σ(I) obs: 3.31 / Num. unique obs: 2739 / CC1/2: 0.6 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.66 Å
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Refine LS restraints |
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LS refinement shell |
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