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- PDB-7cy7: Crystal Structure of CMD1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7cy7
TitleCrystal Structure of CMD1 in complex with DNA
Components
  • DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
  • Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
KeywordsTRANSFERASE / 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
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / DNA / DNA (> 10) / 5-methylcytosine-modifying enzyme 1 / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Chlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, W. / Zhang, T. / Sun, M. / Ding, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530013 China
National Natural Science Foundation of China (NSFC)31800622 China
Chinese Academy of SciencesXDB37030305 China
CitationJournal: 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
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
C: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12113
Polymers107,5093
Non-polymers61210
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint8 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.613, 125.764, 64.034
Angle α, β, γ (deg.)90.000, 102.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / DNA chain , 2 types, 3 molecules ACD

#1: Protein Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1 / 5mC-modifying enzyme 1 / Ten-eleven translocation 1 gene protein homolog / CrTET1


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: 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 DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')


Mass: 4297.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 412 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 60566 / % possible obs: 96.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.8
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / Num. unique obs: 3028 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CY4

7cy4


Resolution: 2.15→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.678 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 3035 5 %RANDOM
Rwork0.1879 ---
obs0.1896 57529 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.11 Å2 / Biso mean: 40.4 Å2 / Biso min: 12.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å2-0 Å2-0.62 Å2
2---3.82 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.15→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 327 37 402 7390
Biso mean--53.57 37.78 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197185
X-RAY DIFFRACTIONr_bond_other_d0.0020.026697
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9089815
X-RAY DIFFRACTIONr_angle_other_deg0.993315407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81524.533289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.943151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4791535
X-RAY DIFFRACTIONr_chiral_restr0.0550.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021628
X-RAY DIFFRACTIONr_rigid_bond_restr3.986313881
X-RAY DIFFRACTIONr_sphericity_free26.6095124
X-RAY DIFFRACTIONr_sphericity_bonded20.093513981
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 163 -
Rwork0.288 2825 -
all-2988 -
obs--62.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0451-0.00630.03850.0023-0.00220.04830.0047-0.0022-0.00130.0025-0.0028-0.0009-0.0048-0.0072-0.00190.04540.00360.01890.13830.00020.088467.465817.6997147.9492
20.8295-2.4629-0.64167.3371.9250.51770.0260.0259-0.1199-0.1577-0.09940.3662-0.0839-0.04050.07340.15090.04270.03230.09890.0080.0921478.357438.431146.9184
30.6365-0.98520.01071.5262-0.01650.0044-0.0416-0.03290.05340.0640.039-0.0896-0.0199-0.00220.00260.09460.0234-0.03090.1578-0.01530.117480.275934.4643149.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-371 - 507
2X-RAY DIFFRACTION2C3 - 11
3X-RAY DIFFRACTION3D1 - 7

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