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- PDB-8jkk: Crystal Structure of the dioxygenase CcTet from Coprinopsis ciner... -

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Basic information

Entry
Database: PDB / ID: 8jkk
TitleCrystal Structure of the dioxygenase CcTet from Coprinopsis cinerea bound to 12bp 5-methylcytosine (5mC) containing duplex DNA
Components
  • 2OGFeDO JBP1/TET oxygenase domain-containing protein
  • DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA demethylase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / macromolecule modification / metal ion binding / : / N-OXALYLGLYCINE / DNA / DNA (> 10) / 2OGFeDO JBP1/TET oxygenase domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation.
Authors: Zhang, L. / Mu, Y. / Li, T. / Hu, J. / Lin, H. / Zhang, L.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2OGFeDO JBP1/TET oxygenase domain-containing protein
B: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
D: 2OGFeDO JBP1/TET oxygenase domain-containing protein
E: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
F: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
G: 2OGFeDO JBP1/TET oxygenase domain-containing protein
H: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
I: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
J: 2OGFeDO JBP1/TET oxygenase domain-containing protein
K: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
L: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,20720
Polymers214,39912
Non-polymers8088
Water16,862936
1
A: 2OGFeDO JBP1/TET oxygenase domain-containing protein
B: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8025
Polymers53,6003
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 2OGFeDO JBP1/TET oxygenase domain-containing protein
E: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
F: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8025
Polymers53,6003
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 2OGFeDO JBP1/TET oxygenase domain-containing protein
H: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
I: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8025
Polymers53,6003
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 2OGFeDO JBP1/TET oxygenase domain-containing protein
K: DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')
L: DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8025
Polymers53,6003
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.569, 127.631, 212.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ADGJ

#1: Protein
2OGFeDO JBP1/TET oxygenase domain-containing protein


Mass: 46283.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (fungus)
Gene: CC1G_05589 / Production host: Escherichia coli (E. coli) / References: UniProt: A8P1J0

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DNA chain , 2 types, 8 molecules BEHKCFIL

#2: DNA chain
DNA (5'-D(P*CP*GP*AP*TP*CP*(5CM)P*GP*CP*TP*AP*CP*G)-3')


Mass: 3637.395 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain
DNA (5'-D(P*CP*GP*TP*AP*GP*CP*TP*GP*AP*TP*CP*G)-3')


Mass: 3678.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 944 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 / N-Oxalylglycine


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


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 104573 / % possible obs: 99.7 % / Redundancy: 13.4 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.052 / Rrim(I) all: 0.19 / Χ2: 1.066 / Net I/σ(I): 3.6 / Num. measured all: 1404090
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.3813.61.342103180.8390.9550.3751.3940.98799.8
2.38-2.4813.71.008103620.8940.9710.281.0470.99299.9
2.48-2.5913.70.799103240.9260.980.2220.830.97199.9
2.59-2.7313.30.589103920.9490.9870.1660.6120.98100
2.73-2.912.60.39104030.9680.9920.1130.4060.97199.8
2.9-3.1214.20.27103950.9870.9970.0740.280.96199.8
3.12-3.44140.166104380.9910.9980.0460.1730.94999.8
3.44-3.9313.30.133104980.9930.9980.0380.1381.16499.7
3.93-4.9513.20.086105260.9950.9990.0240.0890.93899.4
4.95-5012.80.087109170.9790.9950.0260.0911.75699.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→21.98 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 4766 5.02 %
Rwork0.1869 --
obs0.1884 94917 90.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11960 1945 0 936 14841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01614434
X-RAY DIFFRACTIONf_angle_d1.62820013
X-RAY DIFFRACTIONf_dihedral_angle_d26.2045457
X-RAY DIFFRACTIONf_chiral_restr0.1592208
X-RAY DIFFRACTIONf_plane_restr0.012255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.27161110.23652001X-RAY DIFFRACTION61
2.33-2.350.30351100.22642169X-RAY DIFFRACTION66
2.35-2.380.25521320.22562264X-RAY DIFFRACTION69
2.38-2.410.29841360.21862327X-RAY DIFFRACTION70
2.41-2.440.26621250.21132394X-RAY DIFFRACTION74
2.44-2.480.22991250.21772540X-RAY DIFFRACTION76
2.48-2.510.27621360.22552536X-RAY DIFFRACTION78
2.51-2.550.25231650.21892689X-RAY DIFFRACTION81
2.55-2.590.27261400.23052718X-RAY DIFFRACTION84
2.59-2.630.26341960.23052847X-RAY DIFFRACTION87
2.63-2.680.29541330.22362977X-RAY DIFFRACTION90
2.68-2.730.26271560.2263103X-RAY DIFFRACTION94
2.73-2.780.30811470.22043114X-RAY DIFFRACTION94
2.78-2.840.23151720.21083115X-RAY DIFFRACTION94
2.84-2.90.2361740.21463290X-RAY DIFFRACTION100
2.9-2.960.25831640.21273301X-RAY DIFFRACTION100
2.96-3.040.27141700.21233291X-RAY DIFFRACTION100
3.04-3.120.23751830.20943306X-RAY DIFFRACTION100
3.12-3.210.23111510.19893343X-RAY DIFFRACTION100
3.21-3.310.21161670.19493287X-RAY DIFFRACTION100
3.31-3.430.22641770.18773317X-RAY DIFFRACTION100
3.43-3.570.2131760.18073302X-RAY DIFFRACTION100
3.57-3.730.2391830.19333278X-RAY DIFFRACTION99
3.73-3.930.17171730.16793315X-RAY DIFFRACTION99
3.93-4.170.19521900.15863262X-RAY DIFFRACTION98
4.17-4.490.16071990.1473325X-RAY DIFFRACTION100
4.49-4.940.17421720.14623376X-RAY DIFFRACTION100
4.94-5.640.21431640.16993398X-RAY DIFFRACTION100
5.64-7.070.18131660.17923457X-RAY DIFFRACTION100
7.07-21.980.15651730.163509X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -64.9102 Å / Origin y: -29.8562 Å / Origin z: -52.4847 Å
111213212223313233
T0.2113 Å20.0343 Å2-0.0023 Å2-0.142 Å20.0058 Å2--0.215 Å2
L0.2094 °2-0.0015 °2-0.0039 °2-0.0104 °20.0762 °2--0.3396 °2
S0.0012 Å °0.0631 Å °0.0073 Å °-0.0452 Å °-0.0338 Å °0.0239 Å °-0.0448 Å °-0.0004 Å °0.0295 Å °
Refinement TLS groupSelection details: all

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