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- PDB-6lct: Crystal structure of catalytic inactive chloroplast resolvase NtM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lct | ||||||
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Title | Crystal structure of catalytic inactive chloroplast resolvase NtMOC1 in complex with Holliday junction | ||||||
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![]() | HYDROLASE/DNA / chloroplast / resolvase / Holliday junction / PLANT PROTEIN / HYDROLASE / HYDROLASE-DNA complex | ||||||
Function / homology | Holliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / DNA / DNA (> 10) / Uncharacterized protein LOC107823122![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, J.J. / Hong, S.X. / Guan, Z.Y. / Yin, P. | ||||||
![]() | ![]() Title: Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1. Authors: Yan, J. / Hong, S. / Guan, Z. / He, W. / Zhang, D. / Yin, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.1 KB | Display | ![]() |
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PDB format | ![]() | 168.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kvnC ![]() 6kvoSC ![]() 6lcmC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 18199.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 4 types, 4 molecules CDEF
#2: DNA chain | Mass: 5598.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5498.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 5470.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 5497.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 11 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #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: 3.18 Å3/Da / Density % sol: 61.36 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, Sodium acetate trihydrate, 3-Methyl-1,5-Pentane Diol, D-sorbitol |
-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: Mar 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→45.35 Å / Num. obs: 24991 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 83.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.55→2.66 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2962 / CC1/2: 0.812 / Rpim(I) all: 0.418 / Rrim(I) all: 0.789 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KVO Resolution: 2.55→45.35 Å / SU ML: 0.3925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9102
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→45.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -33.647013864 Å / Origin y: 16.0341433139 Å / Origin z: -15.3068916811 Å
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Refinement TLS group | Selection details: all |