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Open data
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Basic information
Entry | Database: PDB / ID: 7cy6 | ||||||||||||
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Title | Crystal Structure of CMD1 in complex with 5mC-DNA | ||||||||||||
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![]() | TRANSFERASE / TET / Vitamin C / dioxygenase / 5gmC / DNA modification / 2-oxoglutarate | ||||||||||||
Function / homology | ![]() methylcytosine to 5-glyceryl-methylcytosine dioxygenase activity / regulation of photosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / 5-methylcytosine catabolic process / dioxygenase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...methylcytosine to 5-glyceryl-methylcytosine dioxygenase activity / regulation of photosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / 5-methylcytosine catabolic process / dioxygenase activity / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / iron ion binding / DNA damage response / membrane / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
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 | ![]() | 396.3 KB | Display | ![]() |
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PDB format | ![]() | 313.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cy4SC ![]() 7cy5C ![]() 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
-Protein / DNA chain , 2 types, 3 molecules ACD
#1: Protein | Mass: 98913.453 Da / Num. of mol.: 1 / 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.) ![]() ![]() ![]() ![]() Gene: CMD1, CHLRE_12g553400v5 / Production host: ![]() ![]() References: UniProt: A0A376KDN7, UniProt: A0A2K3D5Z7, UniProt: P0AEX9*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous |
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#2: DNA chain | Mass: 4311.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 454 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-FE2 / | #6: 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: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000 |
-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: May 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50.01 Å / Num. obs: 62383 / % possible obs: 96.6 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.1→2.15 Å / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3199 / CC1/2: 0.78 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CY4 Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.569 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / 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: 149.88 Å2 / Biso mean: 35.981 Å2 / Biso min: 11.47 Å2
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Refinement step | Cycle: final / Resolution: 2.1→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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