+Open data
-Basic information
Entry | Database: PDB / ID: 7cy8 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of CMD1 in complex with 5mC-DNA and vitamin C | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSFERASE / TET / Vitamin C / dioxygenase / 5gmC / DNA modification / 2-oxoglutarate | ||||||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) Chlamydomonas reinhardtii (plant) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Li, W. / Zhang, T. / Sun, M. / Ding, J. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7cy8.cif.gz | 374.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7cy8.ent.gz | 293.8 KB | Display | PDB format |
PDBx/mmJSON format | 7cy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cy8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7cy8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7cy8_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 7cy8_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cy8 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cy8 | HTTPS FTP |
-Related structure data
Related structure data | 7cy4SC 7cy5C 7cy6C 7cy7C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / DNA chain / Sugars , 3 types, 4 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.) Escherichia coli (E. coli), (gene. exp.) Chlamydomonas reinhardtii (plant) Gene: malE, DJ492_13065, EPS91_05465, FV295_14110, GKG08_19970, GKG09_19840, GKG11_20010, GKG22_19675, GKG29_19885, NCTC8450_00456, CMD1, CHLRE_12g553400v5 Production host: Escherichia coli (E. coli) References: UniProt: A0A376KDN7, UniProt: A0A2K3D5Z7, UniProt: P0AEX9*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous | ||
---|---|---|---|
#2: DNA chain | Mass: 4311.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Sugar | ChemComp-ASC / | |
-Non-polymers , 4 types, 202 molecules
#4: Chemical | #5: Chemical | ChemComp-IPA / | #6: Chemical | ChemComp-FE2 / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
---|---|
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: 173 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.28 Å / Num. obs: 35155 / % possible obs: 94.6 % / Redundancy: 4.7 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1758 / CC1/2: 0.53 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CY4 Resolution: 2.4→49.28 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 22.816 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 176.31 Å2 / Biso mean: 49.153 Å2 / Biso min: 13.64 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→49.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|