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- PDB-4lt5: Structure of a Naegleria Tet-like dioxygenase in complex with 5-m... -

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Basic information

Entry
Database: PDB / ID: 4lt5
TitleStructure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA
Components
  • (DNA) x 2
  • Naegleria Tet-like dioxygenase
KeywordsOXIDOREDUCTASE/DNA / 5-METHYLCYTOSINE / DIOXYGENASE-DNA COMPLEX / 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
: / N-OXALYLGLYCINE / DNA / DNA (> 10) / Tet-like dioxygenase 1
Similarity search - Component
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.893 Å
AuthorsHashimoto, H. / Pais, J.E. / Zhang, X. / Saleh, L. / Fu, Z.Q. / Dai, N. / Correa, I.R. / Roberts, R.J. / Zheng, Y. / Cheng, X.
CitationJournal: Nature / Year: 2014
Title: Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.
Authors: Hashimoto, H. / Pais, J.E. / Zhang, X. / Saleh, L. / Fu, Z.Q. / Dai, N. / Correa, I.R. / Zheng, Y. / Cheng, X.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 5, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 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.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: Naegleria Tet-like dioxygenase
B: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10718
Polymers45,9623
Non-polymers1,14515
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.954, 108.648, 166.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-412-

SO4

21A-560-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Naegleria Tet-like dioxygenase


Mass: 37374.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_55029 / Plasmid: pXC1010 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-Gold cells / References: UniProt: D2W6T1

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA


Mass: 4293.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesis
#3: DNA chain DNA


Mass: 4293.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesis

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Non-polymers , 5 types, 115 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-OGA / N-OXALYLGLYCINE


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.1370.2
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, sitting drop5.52 M ammonium sulfate, 0.1 M BisTris-HCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
2892vapor diffusion, sitting drop820% (w/v) polyethylene glycol 3350, and 0.2 M sodium citrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 22-BM11
SYNCHROTRONAPS 22-ID20.91931
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDNov 16, 2012Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
MARMOSAIC 300 mm CCD2CCDFeb 6, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal - liquor nitrogen cooledSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.919311
ReflectionResolution: 2.89→30 Å / Num. obs: 17328 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 67.98 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.8
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1699 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SGXPROmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.893→29.547 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 869 5.02 %Random
Rwork0.1933 ---
obs0.1944 17321 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.893→29.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 570 67 100 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062894
X-RAY DIFFRACTIONf_angle_d0.6754027
X-RAY DIFFRACTIONf_dihedral_angle_d20.0721097
X-RAY DIFFRACTIONf_chiral_restr0.041435
X-RAY DIFFRACTIONf_plane_restr0.003412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8933-3.07440.31941730.29382641264199
3.0744-3.31150.262870.252127472747100
3.3115-3.64420.28561740.227827022702100
3.6442-4.17030.23011740.189627082708100
4.1703-5.24930.1717870.15428052805100
5.2493-29.54810.16611740.17628492849100

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