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- PDB-7w5p: Crystal Structure of the dioxygenase CcTet from Coprinopsis ciner... -

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Basic information

Entry
Database: PDB / ID: 7w5p
TitleCrystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp N6-methyldeoxyadenine (6mA) containing duplex DNA
Components
  • CcTet
  • DNA
  • DNA (12-MER)
KeywordsDNA BINDING PROTEIN/DNA / dioxygenase / 5-methylcytosin oxidation / N6-methyldeoxyadenine demethylation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / dioxygenase activity / metal ion binding / : / N-OXALYLGLYCINE / DNA / DNA (> 10) / 2OGFeDO JBP1/TET oxygenase domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMu, Y.J. / Zhang, L. / Zhang, L.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853118 China
National Natural Science Foundation of China (NSFC)22107067 China
National Natural Science Foundation of China (NSFC)22077081 China
National Natural Science Foundation of China (NSFC)21722802 China
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Authors: Mu, Y. / Zhang, L. / Hu, J. / Zhou, J. / Lin, H.W. / He, C. / Chen, H.Z. / Zhang, L.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CcTet
B: DNA (12-MER)
C: DNA
D: CcTet
E: DNA (12-MER)
F: DNA
G: CcTet
H: CcTet
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,01016
Polymers207,2028
Non-polymers8088
Water15,601866
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-59 kcal/mol
Surface area66080 Å2
Unit cell
Length a, b, c (Å)104.788, 105.198, 196.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ADGH

#1: Protein
CcTet


Mass: 48117.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_05589 / Production host: Escherichia coli (E. coli) / References: UniProt: A8P1J0

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (12-MER)


Mass: 3661.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 874 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 20% PEG 8000

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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 6M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 96239 / % possible obs: 99.5 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.116 / Χ2: 1.037 / Net I/σ(I): 4.4 / Num. measured all: 1309069
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3414.10.72647670.8630.1980.7530.96299.8
2.34-2.38140.6247500.9020.170.6430.96699.7
2.38-2.43140.57547620.910.1580.5960.96999.9
2.43-2.4813.80.50447710.9250.1390.5240.96899.9
2.48-2.5313.80.45447640.9440.1250.4720.97199.9
2.53-2.5913.70.40147940.9520.1110.4160.96599.7
2.59-2.6613.60.3547490.960.0980.3640.9799.3
2.66-2.7313.30.29747430.970.0840.3090.96399.4
2.73-2.8112.10.25147440.9750.0740.2620.96598.6
2.81-2.913.60.20847750.9830.0580.2160.97599.3
2.9-314.30.17648190.9910.0480.1820.96299.7
3-3.1214.30.15547670.9910.0420.1610.95799.7
3.12-3.2614.20.13348120.9920.0360.1380.96499.6
3.26-3.44140.11648010.9940.0320.120.9999.7
3.44-3.6513.70.10148360.9940.0280.1051.00599.9
3.65-3.9313.20.09448120.9940.0270.0981.02599.2
3.93-4.3312.50.08848190.9940.0250.0921.09999
4.33-4.9514.10.07949260.9960.0220.0821.1100
4.95-6.2413.70.07749300.9950.0220.080.9799.7
6.24-5012.20.08450980.9550.0260.0882.06998.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VPN

7vpn


Resolution: 2.3→49.18 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 4827 5.03 %
Rwork0.2277 91081 -
obs0.2292 95908 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.52 Å2 / Biso mean: 34.4591 Å2 / Biso min: 10.16 Å2
Refinement stepCycle: final / Resolution: 2.3→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11828 990 44 866 13728
Biso mean--24.43 35.02 -
Num. residues----1556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.33931570.28532798295593
2.33-2.360.30031330.27092997313099
2.36-2.380.32761760.26663028320499
2.38-2.420.31411350.269330123147100
2.42-2.450.31991580.274130613219100
2.45-2.480.29751440.271230113155100
2.48-2.520.34381620.274930243186100
2.52-2.550.29651330.275530803213100
2.55-2.590.36741490.269230243173100
2.59-2.640.29641780.26312997317599
2.64-2.680.30931540.26153023317799
2.68-2.730.29191730.26262975314899
2.73-2.780.3121570.25653029318699
2.78-2.840.28021490.24912989313898
2.84-2.90.2891620.255630573219100
2.9-2.970.30651750.255330283203100
2.97-3.040.29151660.25330043170100
3.04-3.120.28721500.246430563206100
3.13-3.220.24591800.243630073187100
3.22-3.320.2461650.237330693234100
3.32-3.440.28381800.222830243204100
3.44-3.580.25311430.21230793222100
3.58-3.740.25441810.218230713252100
3.74-3.940.21851490.2093037318699
3.94-4.180.20811750.19923039321498
4.18-4.510.21061910.184630623253100
4.51-4.960.23461330.174631543287100
4.96-5.680.21061800.196730763256100
5.68-7.150.21411490.20473130327998
7.15-49.180.21351900.21243140333096

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