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- PDB-4gyz: Mus Musculus Tdp2 Bound to dAMP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 4gyz
TitleMus Musculus Tdp2 Bound to dAMP and Mg2+
ComponentsTyrosyl-DNA phosphodiesterase 2
KeywordsHYDROLASE / protein-DNA complex / DNA repair / 5'-DNA end processing / endonuclease/exonuclease/phosphatase domain / EEP domain / 5'-DNA end recognition
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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Tyrosyl-DNA phosphodiesterase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.556 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 / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
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_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_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: Tyrosyl-DNA phosphodiesterase 2
D: Tyrosyl-DNA phosphodiesterase 2
E: Tyrosyl-DNA phosphodiesterase 2
F: Tyrosyl-DNA phosphodiesterase 2
G: Tyrosyl-DNA phosphodiesterase 2
H: Tyrosyl-DNA phosphodiesterase 2
I: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,41928
Polymers260,0119
Non-polymers2,40719
Water7,134396
1
A: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2463
Polymers28,8901
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2463
Polymers28,8901
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2814
Polymers28,8901
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2814
Polymers28,8901
Non-polymers3913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2463
Polymers28,8901
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0093
Polymers28,8901
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9142
Polymers28,8901
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2463
Polymers28,8901
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9503
Polymers28,8901
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.347, 169.326, 184.959
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 , 1 types, 9 molecules ABCDEFGHI

#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.: 9 / Fragment: catalytic domain (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

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Non-polymers , 5 types, 415 molecules

#2: Chemical
ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: PEG 6000, 10mM dAMP, 100mM MES, 10mM MgCl2, pH 6.0, 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: Feb 22, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 84985 / Num. obs: 82947 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.8 / Redundancy: 5.3 % / Rmerge(I) obs: 0.105 / Χ2: 0.992 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.644.70.5179130.915192.1
2.64-2.754.80.39781740.979194.7
2.75-2.874.80.30782351.006196.3
2.87-3.024.90.24284631.007198
3.02-3.215.10.1785410.991199
3.21-3.465.20.12285920.997199.5
3.46-3.815.50.09786641.011199.7
3.81-4.365.80.08986971.015199.8
4.36-5.495.90.08987820.985199.6
5.49-505.80.06489240.998197.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
REFMACphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.556→49.977 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 4266 5.03 %random
Rwork0.1912 ---
obs0.1927 82353 97.02 %-
all-84882 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.144 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 155.28 Å2 / Biso mean: 52.0023 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-1.7915 Å20 Å2-0 Å2
2--3.7875 Å20 Å2
3----5.5789 Å2
Refinement stepCycle: LAST / Resolution: 2.556→49.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17532 0 149 396 18077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d0.6
X-RAY DIFFRACTIONf_bond_d0.004
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)
12.78510.11360.56383.29590.2482.86830.0193-0.16760.028-0.0694-0.03430.1356-0.1608-0.2904-0.00220.16380.0114-0.03560.1087-0.00260.112127.880665.450341.6651
22.0193-0.7913-0.15612.8310.40413.29510.09260.11640.1633-0.4259-0.0860.0132-0.99310.04630.0390.465-0.0958-0.00910.0889-0.0450.146930.719696.796757.3337
32.10060.06350.24121.8591-0.08573.2378-0.0563-0.0815-0.1299-0.04160.00990.0353-0.0496-0.02020.03760.09430.04590.02080.15290.00130.18328.072178.179993.6995
43.3129-0.4325-0.40381.89510.4191.35160.20030.10580.1676-0.4195-0.20110.1931-0.2468-0.02990.00110.41490.097-0.11290.1511-0.05190.191492.5527110.293580.7431
52.343-0.1506-0.23353.09681.15772.7234-0.07960.0611-0.0062-0.0230.05810.0017-0.09080.050.02660.10030.0531-0.00640.1804-0.08650.146864.2817118.517934.8797
63.4126-0.24791.16981.583-0.06852.01650.13340.0307-0.35790.6472-0.3119-0.13180.0551.2126-0.10840.0293-0.1989-0.27380.68250.12390.223263.184670.090861.7204
72.49350.4002-0.60282.1896-0.62732.5744-0.0491-0.2301-0.23650.0004-0.00880.02310.3260.00080.02980.160.0524-0.00840.25520.00160.249778.200781.910426.2297
84.38311.3243-1.21722.808-0.38163.8885-0.09820.42460.0685-0.05190.0860.05290.0376-0.1330.02390.15970.01830.02440.33870.08470.237180.362366.4935100.0476
93.16450.01570.93162.73881.05883.64510.3879-0.0777-0.36140.0297-0.30260.25350.514-0.4251-0.0330.3036-0.0043-0.10430.2206-0.05460.177457.5198118.861276.3463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA123 - 370
2X-RAY DIFFRACTION2chain BB121 - 369
3X-RAY DIFFRACTION3chain CC122 - 369
4X-RAY DIFFRACTION4chain DD122 - 369
5X-RAY DIFFRACTION5chain EE122 - 370
6X-RAY DIFFRACTION6chain FF122 - 367
7X-RAY DIFFRACTION7chain GG123 - 368
8X-RAY DIFFRACTION8chain HH123 - 369
9X-RAY DIFFRACTION9chain II123 - 368

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