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- PDB-7cy4: Crystal Structure of CMD1 in apo form -

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Basic information

Entry
Database: PDB / ID: 7cy4
TitleCrystal Structure of CMD1 in apo form
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 / 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
CITRIC ACID / : / Maltodextrin-binding protein / 5-methylcytosine-modifying enzyme 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Chlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)99,1613
Polymers98,9131
Non-polymers2482
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-12 kcal/mol
Surface area35600 Å2
Unit cell
Length a, b, c (Å)154.677, 123.573, 64.206
Angle α, β, γ (deg.)90.000, 103.160, 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 / dioxygenase / 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 (strain B / BL21-DE3) (bacteria), (gene. exp.) Chlamydomonas reinhardtii (plant)
Strain: B / BL21-DE3 / Gene: ECBD_4002, CMD1, CHLRE_12g553400v5 / Plasmid: pET30a-V28E4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140NCD0, 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 / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2% (v/v) tacsimate, pH 5.0, 0.1 M sodium citrate, pH 5.6, 16% (w/v) 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: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→47.77 Å / Num. obs: 48745 / % possible obs: 94.3 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2437 / CC1/2: 0.56 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 16.282 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1996 4.2 %RANDOM
Rwork0.1797 ---
obs0.1815 45661 80.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.2 Å2 / Biso mean: 54.547 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å20.13 Å2
2---2.05 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 2.2→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 14 223 6746
Biso mean--99.37 50.02 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196678
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9549087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13224.555281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.238151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3931534
X-RAY DIFFRACTIONr_chiral_restr0.070.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215094
X-RAY DIFFRACTIONr_rigid_bond_restr4.336676
X-RAY DIFFRACTIONr_sphericity_free15.135581
X-RAY DIFFRACTIONr_sphericity_bonded34.46856677
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 79 -
Rwork0.318 1775 -
all-1854 -
obs--42.81 %
Refinement TLS params.Method: refined / Origin x: 35.3432 Å / Origin y: 26.3715 Å / Origin z: 22.8985 Å
111213212223313233
T0.0113 Å20.0016 Å20.0042 Å2-0.0889 Å2-0.0024 Å2--0.0027 Å2
L0.149 °20.0053 °20.0927 °2-0.0165 °20.0352 °2--0.1477 °2
S-0.0014 Å °0.0088 Å °0.0086 Å °-0.0014 Å °-0.0018 Å °0.0024 Å °-0.0208 Å °-0.0135 Å °0.0032 Å °

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