+Open data
-Basic information
Entry | Database: PDB / ID: 7cy5 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of CMD1 in complex with vitamin C | ||||||||||||
Components | Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1 | ||||||||||||
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 / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / dioxygenase activity ...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 / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / dioxygenase activity / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7cy5.cif.gz | 364.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7cy5.ent.gz | 290.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cy5 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cy5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7cy4SC 7cy6C 7cy7C 7cy8C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Escherichia coli (E. coli), (gene. exp.) Chlamydomonas reinhardtii (plant) Plasmid: pET30a-V28E1 / Gene: CMD1, CHLRE_12g553400v5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A376KDN7, UniProt: A0A2K3D5Z7, UniProt: P0AEX9*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-FE / | ||||
#3: Sugar | ChemComp-ASC / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
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: 0.9785 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 35.1771 Å / Origin y: 25.8259 Å / Origin z: 23.4049 Å
|