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- PDB-8kfv: Crystal structure of ZmMOC1 K229A in complex with a nicked Hollid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kfv | ||||||
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Title | Crystal structure of ZmMOC1 K229A 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.9 KB | Display | ![]() |
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PDB format | ![]() | 81.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kfrC ![]() 8kfsC ![]() 8kftC ![]() 8kfuC ![]() 8kfwC ![]() 6jrgS S: Starting model for refinement 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: 17558.018 Da / Num. of mol.: 2 / Mutation: K229A 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, 124 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 | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M MES pH 6.0, 35% Polyethylene glycol 400 |
-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: Nov 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 28137 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.182 / Net I/σ(I): 16.28 |
Reflection shell | Resolution: 2.19→2.26 Å / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2778 / CC1/2: 0.635 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JRG Resolution: 2.19→32.41 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.18 / Stereochemistry target values: ML
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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 max: 100.33 Å2 / Biso mean: 34.4392 Å2 / Biso min: 12.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→32.41 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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