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- PDB-4gz2: Mus Musculus Tdp2 excluded ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 4gz2
TitleMus Musculus Tdp2 excluded ssDNA complex
Components
  • DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
  • Tyrosyl-DNA phosphodiesterase 2
Keywordshydrolase/dna / protein-DNA complex / DNA repair / 5'-DNA end processing / endonuclease/exonuclease/phosphatase domain / EEP domain / 5'-DNA end recognition / hydrolase-dna complex
Function / homology
Function and homology information


tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / single-stranded DNA binding ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / single-stranded DNA binding / manganese ion binding / endonuclease activity / nucleolus / magnesium ion binding / cytoplasm
Similarity search - Function
Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DNA / DNA (> 10) / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchellenberg, M.J. / Williams, R.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Authors: Schellenberg, M.J. / Appel, C.D. / Adhikari, S. / Robertson, P.D. / Ramsden, D.A. / Williams, R.S.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Jan 2, 2013Group: Database references
Revision 1.4Jul 22, 2020Group: Database references / Derived calculations
Category: ndb_struct_na_base_pair_step / pdbx_struct_assembly ...ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _ndb_struct_na_base_pair_step.twist / _struct_ref_seq_dif.details
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_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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,98810
Polymers64,7994
Non-polymers1896
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-59 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.483, 42.972, 107.951
Angle α, β, γ (deg.)90.000, 95.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosyl-DNA phosphodiesterase 2 / Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ...Tyr-DNA phosphodiesterase 2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / TRAF and TNF receptor-associated protein


Mass: 28776.998 Da / Num. of mol.: 2 / Fragment: unp residues 118-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: DNA chain DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 3622.380 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 22% PEG 3350, 100mM Tris, 250mM Mg(CO2)2, pH 8.5 , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 46693 / Num. obs: 45439 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.119 / Χ2: 2.833 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.922.30.40444191.679193.6
1.92-1.992.50.32545541.85196.2
1.99-2.082.80.29446331.808197
2.08-2.193.10.26446571.802197.4
2.19-2.333.30.2446561.596197.8
2.33-2.513.50.19846901.804198.1
2.51-2.763.50.15247132.651198.4
2.76-3.163.50.11947303.106198.8
3.16-3.993.40.09647914.217198.9
3.99-503.40.08448504.68197.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.472 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8342 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 2364 5.07 %random
Rwork0.2054 ---
obs0.2075 45110 96.74 %-
all-46631 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.818 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 94.88 Å2 / Biso mean: 27.8231 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.2931 Å2-0 Å2-0.0647 Å2
2---0.0833 Å20 Å2
3----0.2098 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 480 10 434 4844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014691
X-RAY DIFFRACTIONf_angle_d1.0276500
X-RAY DIFFRACTIONf_chiral_restr0.061717
X-RAY DIFFRACTIONf_plane_restr0.004746
X-RAY DIFFRACTIONf_dihedral_angle_d16.6371786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8424-1.880.31451370.27012181231883
1.88-1.92090.30041270.25482531265895
1.9209-1.96550.27751250.22192595272096
1.9655-2.01470.25361250.21252552267797
2.0147-2.06910.23971330.19912623275697
2.0691-2.130.30481290.20392606273597
2.13-2.19870.22831420.19732573271597
2.1987-2.27720.2611240.19392650277498
2.2772-2.36830.25581470.20222614276198
2.3683-2.4760.25831400.19742630277098
2.476-2.60640.22951420.20422623276598
2.6064-2.76950.22931440.19872656280098
2.7695-2.9830.25021380.20642659279799
2.983-3.28250.25161670.19682648281599
3.2825-3.75610.20431360.19462696283299
3.7561-4.72660.21811400.18542708284899
4.7266-24.47420.26691680.2352722289098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9121-0.30290.2031.3846-0.19781.438-0.01210.1147-0.0297-0.19550.03810.0534-0.0061-0.0475-0.0180.187-0.0085-0.01730.1014-0.01040.084-6.813-11.4818-13.438
21.2429-0.06670.06271.0397-0.0931.19580.0014-0.0062-0.0092-0.00250.0318-0.13050.01930.13780.01790.065-0.00240.01520.0760.00040.1138-41.407310.7628-47.1203
30.9361-0.9563-0.03111.6986-1.1544.4460.0573-0.1382-0.45780.30240.16720.21880.05-0.3221-0.21090.30.0355-0.04180.25460.10460.2411-38.11111.5749-22.8948
42.001-0.5401-1.29161.7458-0.35111.13980.0334-0.3161-0.02760.23720.18680.1548-0.20120.09370.20430.3530.1185-0.06590.29460.05430.2586-31.0475-2.2321-15.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA122 - 369
2X-RAY DIFFRACTION2chain BB122 - 369
3X-RAY DIFFRACTION3chain CC1 - 12
4X-RAY DIFFRACTION4chain DD1 - 12

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