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- PDB-4gz0: Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex -

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Basic information

Entry
Database: PDB / ID: 4gz0
TitleMus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex
Components
  • DNA (5'-D(P*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 / EEP / 5'-end recognition / nuclear / HYDROLASE / 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 / nuclear body / nucleolus / magnesium ion binding / nucleoplasm / nucleus / 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
6-aminohexan-1-ol / ACETATE ION / DNA / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 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 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Tyrosyl-DNA phosphodiesterase 2
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,652153
Polymers189,63612
Non-polymers9,016141
Water18,7361040
1
A: Tyrosyl-DNA phosphodiesterase 2
D: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,57033
Polymers31,6062
Non-polymers1,96431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 2
C: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26628
Polymers31,6062
Non-polymers1,66026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Tyrosyl-DNA phosphodiesterase 2
F: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26328
Polymers31,6062
Non-polymers1,65726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Tyrosyl-DNA phosphodiesterase 2
H: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,76920
Polymers31,6062
Non-polymers1,16318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Tyrosyl-DNA phosphodiesterase 2
J: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,01424
Polymers31,6062
Non-polymers1,40922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Tyrosyl-DNA phosphodiesterase 2
L: DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,76920
Polymers31,6062
Non-polymers1,16318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.900, 121.100, 167.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 12 molecules ABEKGICDFLHJ

#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: 28890.156 Da / Num. of mol.: 6 / Fragment: unp residues 118-370
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(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2715.799 Da / Num. of mol.: 6 / Source method: obtained synthetically

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Non-polymers , 4 types, 1181 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 113 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-6AH / 6-aminohexan-1-ol


Mass: 117.189 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 45% ethylene glycol, 100mM sodium acetate, 5% PEG 1000, pH 4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8266 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 4, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 131004 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.1 / Redundancy: 3 % / Rmerge(I) obs: 0.079 / Χ2: 1.001 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.90.535135690.994199
2.18-2.262.90.402135891.005199
2.26-2.3730.315135961.01198.9
2.37-2.4930.23135560.999198.6
2.49-2.6530.171135800.992198.5
2.65-2.8530.12135411.002198.1
2.85-3.1430.09135420.999197.9
3.14-3.5930.08135541.006197.4
3.59-4.5230.065136391.005197.4
4.52-5030.057136000.996194.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.113→42.238 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.27 / σ(F): 0.5 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.193 6588 5.03 %random
Rwork0.16 ---
obs0.1617 130977 95.46 %-
all-137206 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.385 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 221.16 Å2 / Biso mean: 45.3969 Å2 / Biso min: 17.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.1148 Å20 Å20 Å2
2---0.0807 Å2-0 Å2
3---0.1955 Å2
Refinement stepCycle: LAST / Resolution: 2.113→42.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11892 1098 585 1040 14615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.9
X-RAY DIFFRACTIONf_bond_d0.005
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)
11.4226-0.23220.04141.77240.30031.16590.0755-0.0811-0.06210.0857-0.0020.04020.19760.0220.00010.2197-0.0061-0.01530.1669-0.03350.171515.8691-0.9976-25.5747
21.5170.24370.12242.3098-0.2661.2669-0.0559-0.0607-0.1395-0.01850.08060.070.08590.0956-0.00010.2481-0.01830.03490.1825-0.02880.258-36.61344.492-37.049
31.16250.0468-0.13891.05850.0782.41340.0036-0.12350.05290.0020.02250.0843-0.1233-0.04900.1546-0.01270.03140.2009-0.01690.1522-29.281645.5694-15.8225
41.50420.25630.13033.63340.66580.99920.0305-0.00660.21130.073-0.09060.5107-0.1054-0.1274-0.02240.21930.01980.04720.1991-0.0020.3026-22.2588-29.9037-46.7691
51.8561-0.3014-0.40611.88060.36081.0923-0.1128-0.22650.11560.45910.212-0.30620.11030.05670.06950.32060.0836-0.10880.1617-0.0290.2231-78.0799-28.1613-27.1146
62.16130.1702-0.73791.61070.28261.7623-0.1707-0.1549-0.3388-0.0590.067-0.27520.33950.4747-0.03860.22680.10260.0540.46610.00620.2443-56.00996.86976.2937
70.5911-0.36060.80740.252-0.52331.15610.49710.1156-0.1662-0.0699-0.48980.60130.55070.2777-0.07530.5911-0.08490.04880.2532-0.07810.6977-59.7255-8.5285-38.7504
80.2546-0.03820.06461.7932-1.40931.2919-0.47850.3688-0.2248-1.0103-0.88420.15470.62060.0493-1.56190.4791-0.13320.08030.3248-0.25420.3681-0.1155-12.824-43.2338
90.81820.82490.76891.03620.39561.5284-0.4257-1.0029-0.18460.3399-0.6590.14360.3255-0.6633-1.35340.4535-0.16340.16990.7607-0.05660.3216-38.691529.04472.4931
100.1589-0.1272-0.10660.07240.07230.03310.23670.14310.1018-0.0074-0.2579-0.2496-0.4172-0.03350.00110.4487-0.085-0.02080.2952-0.03930.41720.8033-15.9422-43.6215
110.092-0.0381-0.0920.02950.03390.05780.1558-0.17290.3379-0.1621-0.3258-0.3374-0.47170.2654-0.00180.518-0.0516-0.08670.3448-0.09050.8174-59.1452-12.822-39.0418
122.39380.20910.70490.00810.06130.541-0.873-0.35280.7497-0.03650.24940.00560.33410.5701-0.23590.3596-0.12670.07550.6945-0.07980.4154-41.698629.77743.0742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA121 - 370
2X-RAY DIFFRACTION2chain BB121 - 370
3X-RAY DIFFRACTION3chain EE121 - 370
4X-RAY DIFFRACTION4chain GG122 - 370
5X-RAY DIFFRACTION5chain II121 - 370
6X-RAY DIFFRACTION6chain KK122 - 370
7X-RAY DIFFRACTION7chain CC1 - 10
8X-RAY DIFFRACTION8chain DD1 - 10
9X-RAY DIFFRACTION9chain FF1 - 10
10X-RAY DIFFRACTION10chain HH1 - 10
11X-RAY DIFFRACTION11chain JJ1 - 10
12X-RAY DIFFRACTION12chain LL1 - 10

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