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- PDB-4z3c: Zinc finger region of human TET3 in complex with CpG DNA -

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Basic information

Entry
Database: PDB / ID: 4z3c
TitleZinc finger region of human TET3 in complex with CpG DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
  • Methylcytosine dioxygenase
KeywordsDNA Binding protein/DNA / zinc finger / dna-binding / Structural Genomics / Structural Genomics Consortium / SGC / DNA Binding protein-DNA complex
Function / homology
Function and homology information


epigenetic programing of male pronucleus / : / : / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / : / oxidative demethylation / protein O-linked glycosylation / methyl-CpG binding ...epigenetic programing of male pronucleus / : / : / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / : / oxidative demethylation / protein O-linked glycosylation / methyl-CpG binding / male pronucleus / female pronucleus / chromosome / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Methylcytosine dioxygenase TET1/2/3 / Oxygenase domain of the 2OGFeDO superfamily / 2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / Methylcytosine dioxygenase TET3 / Methylcytosine dioxygenase TET3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Dong, A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2017
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_entity_src_syn ...entity_src_gen / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 3, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
B: DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')
C: Methylcytosine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3559
Polymers13,2243
Non-polymers1316
Water1,53185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.616, 54.744, 40.228
Angle α, β, γ (deg.)90.000, 103.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others)
#2: Protein Methylcytosine dioxygenase


Mass: 5897.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TET3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: K9JJH7, UniProt: O43151*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 30% PEG-1500, 0.2 M sodium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.57→39.11 Å / Num. obs: 16318 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 10.4 / Num. measured all: 59473
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.57-1.63.51.071.128488120.4640.66599.8
8.6-39.1130.0427295970.9950.02990.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HP3

4hp3


Resolution: 1.57→39.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2466 / WRfactor Rwork: 0.2132 / FOM work R set: 0.7594 / SU B: 6.238 / SU ML: 0.095 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.0994 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the structure was by molecular replacement using diffraction data collected on an isomorphous sanple. coot was used for interactive model building. Model geometry was assessed with phenix.molprobity.
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 807 5 %RANDOM
Rwork0.2146 15494 --
obs0.2164 16301 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.84 Å2 / Biso mean: 28.058 Å2 / Biso min: 16.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.79 Å2
2---2.39 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 1.57→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms324 486 6 85 901
Biso mean--25.66 34.21 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.014915
X-RAY DIFFRACTIONr_bond_other_d0.0040.02620
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.4561343
X-RAY DIFFRACTIONr_angle_other_deg1.45131452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.984546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9862013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9241573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.509156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02693
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02207
X-RAY DIFFRACTIONr_mcbond_it1.6191.671181
X-RAY DIFFRACTIONr_mcbond_other1.6231.665180
X-RAY DIFFRACTIONr_mcangle_it2.422.492225
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 63 -
Rwork0.31 1149 -
all-1212 -
obs--99.67 %
Refinement TLS params.Method: refined / Origin x: -3.1291 Å / Origin y: 9.615 Å / Origin z: -11.6993 Å
111213212223313233
T0.0442 Å2-0.0097 Å20.0101 Å2-0.1613 Å20.003 Å2--0.0124 Å2
L1.8112 °2-0.5212 °20.0252 °2-3.4037 °2-0.4583 °2--1.2797 °2
S0.0178 Å °-0.0696 Å °-0.0414 Å °0.0688 Å °0.042 Å °0.1972 Å °-0.2308 Å °-0.055 Å °-0.0598 Å °

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