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

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Basic information

Entry
Database: PDB / ID: 4qzh
TitleMouse Tdt, F401A mutant, in complex with a DSB substrate, C-T base pair
Components
  • 5'-D(*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*TP*TP*TP*TP*GP*T)-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: 2.6 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*T)-3'
U: 5'-D(*AP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8818
Polymers51,3584
Non-polymers5234
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-56 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.309, 75.009, 125.611
Angle α, β, γ (deg.)90.00, 97.64, 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*T)-3'


Mass: 2109.405 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 109 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.: 105 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2012 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 16036 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 82.98 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2318 / % possible all: 99.9

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Processing

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

4i2a


Resolution: 2.6→41.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.9126 / SU R Cruickshank DPI: 0.472 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.475 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.252 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 804 5.01 %RANDOM
Rwork0.1964 ---
obs0.1977 16033 99.79 %-
Displacement parametersBiso mean: 82.8 Å2
Baniso -1Baniso -2Baniso -3
1--22.1301 Å20 Å2-4.8921 Å2
2--12.9757 Å20 Å2
3---9.1544 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 351 30 105 3081
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013097HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1314SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it3097HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion2.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
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_contact3367SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2766 142 4.92 %
Rwork0.2265 2743 -
all0.2289 2885 -
obs--99.79 %
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)
12.028-0.96240.76764.37871.06331.90490.03580.4671-0.5274-0.02740.1283-0.5528-0.03950.6118-0.1641-0.27410.1296-0.05640.0258-0.12790.0886-19.286-9.667619.9663
24.39971.6691-0.17561.28890.50272.25270.2939-0.54580.30280.5753-0.2524-0.1951-0.2736-0.0245-0.04150.3088-0.07710.023-0.304-0.0026-0.3088-24.91024.319445.6743
31.5920.65771.62862.0196-1.15372.58060.1325-0.26170.01130.4671-0.16660.6118-0.3775-0.58420.034-0.08330.16490.1351-0.0819-0.08640.0435-41.3883-0.456127.9113
40.93920.57460.95425.46112.56923.3614-0.09710.37030.3398-0.3790.26250.3836-0.45280.2017-0.16540.19550.13430.0181-0.0661-0.0058-0.1577-29.59997.726313.9841
50.5688-2.899-2.19890.00930.50111.1754-0.02580.04090.161-0.0308-0.02670.0577-0.0485-0.18050.05250.17750.02650.1866-0.07950.1091-0.0622-23.168516.530635.3096
61.28580.6884-3.21975.9411-2.84414.54120.01880.1475-0.0495-0.21020.12260.1616-0.2696-0.1333-0.14140.06350.0833-0.04240.0502-0.0127-0.1392-27.16420.60468.3982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|149 - 243}A149 - 243
2X-RAY DIFFRACTION2{A|244 - 431}A244 - 431
3X-RAY DIFFRACTION3{A|432 - 510}A432 - 510
4X-RAY DIFFRACTION4{T|1 - 7}T1 - 7
5X-RAY DIFFRACTION5{U|1 - 6}U1 - 6
6X-RAY DIFFRACTION6{D|1 - 6}D1 - 6

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