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Open data
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Basic information
Entry | Database: PDB / ID: 7cy5 | ||||||||||||
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Title | Crystal Structure of CMD1 in complex with vitamin C | ||||||||||||
![]() | Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1 | ||||||||||||
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Function / homology | ![]() methylcytosine to 5-glyceryl-methylcytosine dioxygenase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, W. / Zhang, T. / Sun, M. / Ding, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1. Authors: Li, W. / Zhang, T. / Sun, M. / Shi, Y. / Zhang, X.J. / Xu, G.L. / Ding, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.2 KB | Display | ![]() |
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PDB format | ![]() | 297 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 839.7 KB | Display | ![]() |
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Full document | ![]() | 845.4 KB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cy4SC ![]() 7cy6C ![]() 7cy7C ![]() 7cy8C 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 98913.453 Da / Num. of mol.: 1 / Fragment: dioxygenase,dioxygenase / Mutation: D108A, K109A, E198A, N199A, E385A, K388A, D389A Source method: isolated from a genetically manipulated source Details: The fusion protein of Maltodextrin-binding protein UNP RESIDUES 27-392), linker, 5-methylcytosine-modifying enzyme 1 (UNP RESIDUES 1-532) and tags Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Plasmid: pET30a-V28E1 / Gene: CMD1, CHLRE_12g553400v5 / Production host: ![]() ![]() ![]() References: UniProt: A0A376KDN7, UniProt: A0A2K3D5Z7, UniProt: P0AEX9*PLUS, ![]() | ||||
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#2: Chemical | ChemComp-FE / ![]() | ||||
#3: Sugar | ChemComp-ASC / ![]() | ||||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow![]() | Temperature: 290 K / Method: evaporation / pH: 5.6 / Details: 2% Tacsimate, 0.1M CIT pH 5.6, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→48.38 Å / Num. obs: 55672 / % possible obs: 95.5 % / Redundancy: 4.9 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2783 / CC1/2: 0.65 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7CY4 Resolution: 2.2→48.38 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.435 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.3 Å2 / Biso mean: 38.512 Å2 / Biso min: 7.58 Å2
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Refinement step | Cycle: final / Resolution: 2.2→48.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 35.1771 Å / Origin y: 25.8259 Å / Origin z: 23.4049 Å
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