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- PDB-5d9y: Crystal structure of TET2-5fC complex -

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Basic information

Entry
Database: PDB / ID: 5d9y
TitleCrystal structure of TET2-5fC complex
Components
  • DNA (5'-D(*AP*CP*TP*GP*TP*(5FC)P*GP*AP*AP*GP*CP*T)-3')
  • DNA (5'-D(*AP*GP*CP*TP*TP*CP*GP*AP*CP*AP*GP*T)-3')
  • Methylcytosine dioxygenase TET2,Methylcytosine dioxygenase TET2
Keywordsoxidoreductase/DNA / 5-methylcytosine dioxygenase / TET2 / 5-formylcytosine / protein-DNA complex / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.971 Å
AuthorsHu, L. / Cheng, J. / Rao, Q. / Li, Z. / Li, J. / Xu, Y.
CitationJournal: Nature / Year: 2015
Title: Structural insight into substrate preference for TET-mediated oxidation.
Authors: Hu, L. / Lu, J. / Cheng, J. / Rao, Q. / Li, Z. / Hou, H. / Lou, Z. / Zhang, L. / Li, W. / Gong, W. / Liu, M. / Sun, C. / Yin, X. / Li, J. / Tan, X. / Wang, P. / Wang, Y. / Fang, D. / Cui, Q. ...Authors: Hu, L. / Lu, J. / Cheng, J. / Rao, Q. / Li, Z. / Hou, H. / Lou, Z. / Zhang, L. / Li, W. / Gong, W. / Liu, M. / Sun, C. / Yin, X. / Li, J. / Tan, X. / Wang, P. / Wang, Y. / Fang, D. / Cui, Q. / Yang, P. / He, C. / Jiang, H. / Luo, C. / Xu, Y.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references / Other
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,1498
Polymers58,7503
Non-polymers3995
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-30 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.154, 87.958, 268.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methylcytosine dioxygenase TET2,Methylcytosine dioxygenase TET2


Mass: 51397.352 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*TP*(5FC)P*GP*AP*AP*GP*CP*T)-3')


Mass: 3690.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*CP*TP*TP*CP*GP*AP*CP*AP*GP*T)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 267 molecules

#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 21% PEGMME2000, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 57919 / % possible obs: 98.9 % / Redundancy: 6 % / Biso Wilson estimate: 24.08 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 0.88 / Net I/av σ(I): 28 / Net I/σ(I): 7.5 / Num. measured all: 242789
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-2.044.70.62437510.8170.2990.6950.97693.2
2.04-2.125.40.49239630.9140.2240.5430.9998.2
2.12-2.225.80.36739910.9480.1630.4030.98199
2.22-2.345.80.2540110.9750.1110.2740.97699.3
2.34-2.486.30.18140700.9840.0780.1980.93199.9
2.48-2.676.20.12740780.990.0550.1390.87799.9
2.67-2.946.10.08140560.9940.0350.0880.85999.5
2.94-3.376.60.05541010.9970.0230.060.848100
3.37-4.246.50.04241240.9970.0180.0460.80299.7
4.24-506.30.03643330.9980.0160.0390.65999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM6

4nm6


Resolution: 1.971→36.767 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 3114 5.38 %
Rwork0.2051 54805 -
obs0.2074 57919 74.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.2 Å2 / Biso mean: 33.6166 Å2 / Biso min: 8.37 Å2
Refinement stepCycle: final / Resolution: 1.971→36.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 488 14 262 4016
Biso mean--24.51 32.43 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093900
X-RAY DIFFRACTIONf_angle_d1.1595364
X-RAY DIFFRACTIONf_chiral_restr0.045580
X-RAY DIFFRACTIONf_plane_restr0.005620
X-RAY DIFFRACTIONf_dihedral_angle_d19.4281517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9705-2.00130.3612570.31005106229
2.0013-2.03410.3174610.29391050111133
2.0341-2.06920.2942750.31268134338
2.0692-2.10680.3099810.29641365144641
2.1068-2.14730.3349890.28751493158245
2.1473-2.19120.3028960.28981713180951
2.1912-2.23880.30841000.27671778187854
2.2388-2.29090.29821150.26232060217560
2.2909-2.34820.31591350.25342164229966
2.3482-2.41160.32491390.24362498263774
2.4116-2.48260.2461460.23872678282481
2.4826-2.56270.29631710.2342887305887
2.5627-2.65430.30441670.2433152331993
2.6543-2.76050.28341760.23973179335596
2.7605-2.88610.29861760.23363210338697
2.8861-3.03820.26431850.227933843569100
3.0382-3.22840.2421790.214433363515100
3.2284-3.47750.23251830.205733383521100
3.4775-3.82720.21921880.17753318350699
3.8272-4.38020.19592000.157433213521100
4.3802-5.51560.20782000.15353312351299
5.5156-36.77320.22721950.16433296349199

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