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- PDB-4nm6: Crystal structure of TET2-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4nm6
TitleCrystal structure of TET2-DNA complex
Components
  • 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'
  • Methylcytosine dioxygenase TET2
KeywordsOXIDOREDUCTASE/DNA / DNA hydroxylation / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


leukocyte differentiation / methylcytosine dioxygenase / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / Specification of primordial germ cells / : / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation ...leukocyte differentiation / methylcytosine dioxygenase / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / Specification of primordial germ cells / : / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation / ferrous iron binding / response to organic cyclic compound / chromosome / cell cycle / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Methylcytosine dioxygenase TET1/2/3 / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / DNA / DNA (> 10) / Methylcytosine dioxygenase TET2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.026 Å
AuthorsHu, L. / Li, Z. / Cheng, J. / Rao, Q. / Gong, W. / Liu, M. / Wang, P. / Xu, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation.
Authors: Hu, L. / Li, Z. / Cheng, J. / Rao, Q. / Gong, W. / Liu, M. / Shi, Y.G. / Zhu, J. / Wang, P. / Xu, Y.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcytosine dioxygenase TET2
B: 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'
C: 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2088
Polymers58,8093
Non-polymers3995
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-18 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.296, 88.186, 262.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein Methylcytosine dioxygenase TET2


Mass: 51454.398 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET2, KIAA1546, Nbla00191 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6N021, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: DNA chain 5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3'


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 136 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN CONSTRUCT COMPRISES UNP RESIDUES 1129-1480 AND 1844-1936 CONNECTED BY A (GGGGS)3 LINKER.

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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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 23% PEG2000 MME, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792, 1.2818
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2013
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.28181
ReflectionResolution: 2.02→50 Å / Num. obs: 34839 / % possible obs: 93.84 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 11.86
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.488 / % possible all: 89.49

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.026→41.805 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1731 4.97 %RANDOM
Rwork0.2024 ---
obs0.2044 34834 93.82 %-
all-34839 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.026→41.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 431 14 131 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083761
X-RAY DIFFRACTIONf_angle_d1.2945159
X-RAY DIFFRACTIONf_dihedral_angle_d20.3441450
X-RAY DIFFRACTIONf_chiral_restr0.087559
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.026-2.0860.27661330.21492605X-RAY DIFFRACTION90
2.086-2.15330.29141560.21192624X-RAY DIFFRACTION92
2.1533-2.23020.28261330.21522710X-RAY DIFFRACTION93
2.2302-2.31950.25271290.22032712X-RAY DIFFRACTION93
2.3195-2.42510.26681230.21642799X-RAY DIFFRACTION95
2.4251-2.55290.27841230.20832766X-RAY DIFFRACTION95
2.5529-2.71280.26771620.22792799X-RAY DIFFRACTION96
2.7128-2.92230.27481580.22612809X-RAY DIFFRACTION96
2.9223-3.21620.25721540.21472799X-RAY DIFFRACTION95
3.2162-3.68140.26061590.20282822X-RAY DIFFRACTION96
3.6814-4.63720.20411640.18182801X-RAY DIFFRACTION95
4.6372-41.81370.2221370.1932857X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -8.9709 Å / Origin y: 0.5435 Å / Origin z: -34.388 Å
111213212223313233
T0.423 Å2-0.0042 Å2-0.1287 Å2-0.4315 Å20.0384 Å2--0.45 Å2
L1.9659 °20.0231 °20.3465 °2-1.6766 °20.3348 °2--1.9267 °2
S0.0016 Å °-0.1304 Å °-0.1602 Å °0.0434 Å °-0.089 Å °0.0845 Å °-0.1744 Å °-0.1692 Å °-0.0118 Å °
Refinement TLS groupSelection details: all

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