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- PDB-4qzg: Mouse Tdt, F401A mutant, in complex with a DSB substrate, C-C bas... -

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Basic information

Entry
Database: PDB / ID: 4qzg
TitleMouse Tdt, F401A mutant, in complex with a DSB substrate, C-C base pair
Components
  • 5'-D(*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*TP*TP*TP*TP*GP*C)-3'
  • DNA nucleotidylexotransferase
KeywordsTRANSFERASE/DNA / Terminal deoxynucleotidyltransferase / nucleus / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / DNA-directed DNA polymerase activity / hydrolase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / DNA-directed DNA polymerase activity / hydrolase activity / DNA repair / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain ...DNA nucleotidylexotransferase (TdT) / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: Embo J. / Year: 2015
Title: Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.
Authors: Gouge, J. / Rosario, S. / Romain, F. / Poitevin, F. / Beguin, P. / Delarue, M.
History
DepositionJul 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 20, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: DNA nucleotidylexotransferase
D: 5'-D(*AP*AP*AP*AP*AP*C)-3'
T: 5'-D(*TP*TP*TP*TP*TP*GP*C)-3'
U: 5'-D(*AP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8668
Polymers51,3434
Non-polymers5234
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-51 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.992, 70.851, 114.893
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA nucleotidylexotransferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / TDT / Terminal transferase


Mass: 45627.914 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: F401A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt / Production host: Escherichia coli (E. coli) / References: UniProt: P09838, DNA nucleotidylexotransferase

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DNA chain , 2 types, 3 molecules DUT

#2: DNA chain 5'-D(*AP*AP*AP*AP*AP*C)-3'


Mass: 1810.258 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*TP*TP*TP*GP*C)-3'


Mass: 2094.394 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 47 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN COMPRISES UNP RESIDUES 132-482 AND 503-530 WITH 483-502 DELETED.

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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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12-17% PEG4000, 9-12% isopropanol, 100 mM sodium acetate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2012
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.75→44.25 Å / Num. obs: 11937 / % possible obs: 99.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 91.35 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1736 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I2A

4i2a


Resolution: 2.75→42.48 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9407 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.283 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 571 4.79 %RANDOM
Rwork0.1876 ---
obs0.1887 11933 99.77 %-
Displacement parametersBiso mean: 80.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.2775 Å20 Å2-0.4494 Å2
2--0.8601 Å20 Å2
3----2.1376 Å2
Refine analyzeLuzzati coordinate error obs: 0.424 Å
Refinement stepCycle: LAST / Resolution: 2.75→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 364 30 43 3032
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1322SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it3128HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion3.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3499SEMIHARMONIC4
LS refinement shellResolution: 2.75→3.01 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2909 141 4.95 %
Rwork0.2242 2708 -
all0.2276 2849 -
obs--99.77 %
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)
13.4693-1.2472-0.12694.8902-0.73633.8730.0382-0.18450.5271-0.2742-0.2330.5178-0.0794-0.56730.1948-0.12880.1527-0.0713-0.01760.0017-0.013-6.00147.685719.1748
27.73842.8247-1.35613.9902-1.84047.3425-0.0262-0.3029-0.0566-0.36550.08260.39160.5532-0.5801-0.0564-0.2655-0.14010.04910.0813-0.1185-0.1982-6.4564-5.337243.668
34.4406-0.6296-1.31060.95670.5634.28290.0636-0.5995-0.26030.084-0.3301-0.12810.20960.48270.2665-0.2609-0.1091-0.06140.22240.0571-0.201514.1774-0.728244.0662
46.1652-2.096-0.73194.18771.36364.93970.2322-0.03020.3959-0.4638-0.2796-0.5975-0.07110.54410.0474-0.01930.1390.0449-0.0450.1283-0.027616.98410.813120.3857
53.3526-2.60662.96170.248-2.75223.5109-0.09660.2373-0.3646-0.40360.2877-0.22760.4972-0.1749-0.19110.31720.0917-0.0314-0.17210.0349-0.25253.432-9.646813.3955
61.2282-0.1932-1.24410-0.2550.55140.00320.0394-0.2113-0.00250.00580.01070.33520.1453-0.0090.0357-0.14410.14850.0234-0.08110.00671.6763-14.500637.1304
73.86683.01612.44768.3154-0.82248.7336-0.00760.04660.1685-0.07180.1311-0.21640.0640.1527-0.12350.09390.1532-0.09560.0749-0.0029-0.18950.0825-3.71048.0597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|148 - 243}A148 - 243
2X-RAY DIFFRACTION2{A|244 - 316}A244 - 316
3X-RAY DIFFRACTION3{A|317 - 452}A317 - 452
4X-RAY DIFFRACTION4{A|453 - 510}A453 - 510
5X-RAY DIFFRACTION5{T|1 - 7}T1 - 7
6X-RAY DIFFRACTION6{U|1 - 6}U1 - 6
7X-RAY DIFFRACTION7{D|1 - 6}D1 - 6

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