7CY8

Crystal Structure of CMD1 in complex with 5mC-DNA and vitamin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report



Literature

Crystal structures of algal TET homologue CMD1 provide insight into the molecular mechanism for vitamin C-derived C5-glyceryl-methylcytosine DNA modification

Li, W.Zhang, T.Sun, M.Shi, Y.Zhang, X.Xu, G.Ding, J.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1A917Escherichia coliChlamydomonas reinhardtii
This entity is chimeric
Mutation(s): 7 
Gene Names: malEDJ492_13065EPS91_05465FV295_14110GKG08_19970GKG09_19840GKG11_20010GKG22_19675GKG29_19885NCTC8450_00456
EC: 1.14.99
Find proteins for A0A376KDN7 (Escherichia coli)
Explore A0A376KDN7 
Go to UniProtKB:  A0A376KDN7
Find proteins for A0A2K3D5Z7 (Chlamydomonas reinhardtii)
Explore A0A2K3D5Z7 
Go to UniProtKB:  A0A2K3D5Z7
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*(5CM)P*GP*CP*GP*CP*GP*GP*GP*A)-3')C, D14synthetic construct
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ASC
    Query on ASC

    Download Ideal Coordinates CCD File 
    A
    ASCORBIC ACID
    C6 H8 O6
    CIWBSHSKHKDKBQ-JLAZNSOCSA-N
     Ligand Interaction
    EDO
    Query on EDO

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    A
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    IPA
    Query on IPA

    Download Ideal Coordinates CCD File 
    A
    ISOPROPYL ALCOHOL
    C3 H8 O
    KFZMGEQAYNKOFK-UHFFFAOYSA-N
     Ligand Interaction
    FE2
    Query on FE2

    Download Ideal Coordinates CCD File 
    A
    FE (II) ION
    Fe
    CWYNVVGOOAEACU-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.40 Å
    • R-Value Free: 0.235 
    • R-Value Work: 0.190 
    • R-Value Observed: 0.192 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 154.488α = 90
    b = 125.646β = 102.96
    c = 64.058γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    XDSdata scaling
    PDB_EXTRACTdata extraction
    XDSdata reduction
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of China (NSFC)China31530013
    National Natural Science Foundation of China (NSFC)China31800622
    Chinese Academy of SciencesChinaXDB37030305

    Revision History 

    • Version 1.0: 2020-12-30
      Type: Initial release