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Yorodumi- PDB-6lcm: Crystal structure of chloroplast resolvase ZmMOC1 with the magic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lcm | ||||||
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Title | Crystal structure of chloroplast resolvase ZmMOC1 with the magic triangle I3C | ||||||
Components | ZmMoc1 | ||||||
Keywords | HYDROLASE / chloroplast / resolvase / Holliday junction / PLANT PROTEIN | ||||||
Function / homology | Holliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / Chem-I3C / Holliday junction resolvase MOC1, chloroplastic Function and homology information | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.5 Å | ||||||
Authors | Yan, J.J. / Hong, S.X. / Guan, Z.Y. / Yin, P. | ||||||
Citation | Journal: Nat Commun / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lcm.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lcm.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lcm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6lcm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6lcm_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 6lcm_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcm ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19082.768 Da / Num. of mol.: 1 / Mutation: E158Q,I211V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 100192759, ZEAMMB73_Zm00001d040409 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4FCI7 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 6571 / % possible obs: 100 % / Redundancy: 33.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 70.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.302 / Num. unique obs: 670 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→45 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 29.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
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Refine LS restraints |
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