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- PDB-7cy5: Crystal Structure of CMD1 in complex with vitamin C -

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Basic information

Entry
Database: PDB / ID: 7cy5
TitleCrystal Structure of CMD1 in complex with vitamin C
ComponentsMaltodextrin-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 / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / 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 / chromosomal 5-methylcytosine DNA demethylation, oxidation pathway / 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 / nucleus / membrane
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
ASCORBIC ACID / CITRIC ACID / : / 5-methylcytosine-modifying enzyme 1 / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Chlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

Deposited unit
A: Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5305
Polymers98,9131
Non-polymers6164
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-13 kcal/mol
Surface area35680 Å2
Unit cell
Length a, b, c (Å)153.846, 126.418, 64.217
Angle α, β, γ (deg.)90.000, 102.270, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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 / 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 / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5.6 / Details: 2% Tacsimate, 0.1M CIT pH 5.6, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CY4

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 2000 3.6 %RANDOM
Rwork0.1811 ---
obs0.1825 53479 91.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.3 Å2 / Biso mean: 38.512 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20.06 Å2
2---2.74 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 2.2→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6563 0 39 402 7004
Biso mean--63.98 38.12 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196759
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9599192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0924.558283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5551534
X-RAY DIFFRACTIONr_chiral_restr0.0850.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215148
X-RAY DIFFRACTIONr_rigid_bond_restr4.79536758
X-RAY DIFFRACTIONr_sphericity_free30.1185159
X-RAY DIFFRACTIONr_sphericity_bonded17.95356857
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 115 -
Rwork0.299 3073 -
all-3188 -
obs--70.75 %
Refinement TLS params.Method: refined / Origin x: 35.1771 Å / Origin y: 25.8259 Å / Origin z: 23.4049 Å
111213212223313233
T0.0129 Å20.0018 Å20.0081 Å2-0.0557 Å2-0.0012 Å2--0.0051 Å2
L0.0256 °2-0.0058 °20.0284 °2-0.002 °2-0.0067 °2--0.0319 °2
S0.0016 Å °-0.0027 Å °0.0001 Å °0.0002 Å °-0.0004 Å °0.0004 Å °-0.0007 Å °-0.0041 Å °-0.0011 Å °

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