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- PDB-5cg8: NgTET1 in complex with 5hmC DNA -

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Basic information

Entry
Database: PDB / ID: 5cg8
TitleNgTET1 in complex with 5hmC DNA
Components
  • DNA (5'-D(*AP*GP*AP*AP*TP*TP*CP*CP*GP*TP*TP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*AP*AP*(5HC)P*GP*GP*AP*AP*TP*TP*CP*T)-3')
  • Tet-like dioxygenase
KeywordsOXIDOREDUCTASE/DNA / dioxygenase / 5-hydroxymethylcytosine / NgTET1 / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


methylcytosine dioxygenase / 5-methylcytosine dioxygenase activity / double-stranded methylated DNA binding / iron ion binding
Similarity search - Function
Double-stranded beta-helix - #30 / Double-stranded beta-helix / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / DNA / DNA (> 10) / Tet-like dioxygenase 1
Similarity search - Component
Biological speciesNaegleria gruberi (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsHashimoto, H. / Pais, J.E. / Dai, N. / Zhang, X. / Zheng, Y. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105132 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA.
Authors: Hashimoto, H. / Pais, J.E. / Dai, N. / Correa, I.R. / Zhang, X. / Zheng, Y. / Cheng, X.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tet-like dioxygenase
B: DNA (5'-D(*AP*GP*AP*AP*TP*TP*CP*CP*GP*TP*TP*CP*CP*A)-3')
C: DNA (5'-D(*TP*GP*GP*AP*AP*(5HC)P*GP*GP*AP*AP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5165
Polymers39,3153
Non-polymers2012
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.802, 107.360, 167.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tet-like dioxygenase


Mass: 30725.766 Da / Num. of mol.: 1 / Fragment: UNP residues 57-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_55029 / Plasmid: pET28b-His-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: D2W6T1

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DNA chain , 2 types, 2 molecules BC

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


Mass: 4239.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*GP*AP*AP*(5HC)P*GP*GP*AP*AP*TP*TP*CP*T)-3')


Mass: 4349.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.8 Å3/Da / Density % sol: 74.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) polyethylene glycol monomethyl ether 550, 10 mM ZnSO4, and 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→27.6 Å / Num. all: 20985 / Num. obs: 20985 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 82.11 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.2
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 10 % / Rmerge(I) obs: 0.977 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LT5

4lt5


Resolution: 2.702→27.554 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 1049 5.01 %Random selection
Rwork0.1909 ---
obs0.1928 20958 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→27.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 570 11 3 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062792
X-RAY DIFFRACTIONf_angle_d0.8923906
X-RAY DIFFRACTIONf_dihedral_angle_d20.361029
X-RAY DIFFRACTIONf_chiral_restr0.099437
X-RAY DIFFRACTIONf_plane_restr0.003407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.84430.36961450.31182761X-RAY DIFFRACTION98
2.8443-3.02230.33111490.28732812X-RAY DIFFRACTION100
3.0223-3.25530.28681480.27092820X-RAY DIFFRACTION100
3.2553-3.58230.27431500.22092837X-RAY DIFFRACTION100
3.5823-4.09920.2651500.19842849X-RAY DIFFRACTION100
4.0992-5.1590.16551520.16052887X-RAY DIFFRACTION100
5.159-27.55560.21121550.16242943X-RAY DIFFRACTION98

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