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- PDB-4qzi: Mouse Tdt, F401A mutant, in complex with a DSB substrate and Zn2+ -

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Basic information

Entry
Database: PDB / ID: 4qzi
TitleMouse Tdt, F401A mutant, in complex with a DSB substrate and Zn2+
Components
  • 5'-D(*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*TP*TP*TP*TP*GP*GP*G)-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 / nucleus / metal ion binding / 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: 2.65 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*GP*G)-3'
U: 5'-D(*AP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3419
Polymers51,7124
Non-polymers6295
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-112 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.700, 71.523, 113.035
Angle α, β, γ (deg.)90.00, 94.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-742-

HOH

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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*GP*G)-3'


Mass: 2463.624 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 75 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 45.31 %
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: 0.9725 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2012
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.65→45 Å / Num. obs: 13390 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 87.56 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1937 / % 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: 2.65→22.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9487 / SU R Cruickshank DPI: 0.734 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.711 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.253 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 660 4.94 %RANDOM
Rwork0.1853 ---
obs0.1862 13373 99.52 %-
Displacement parametersBiso mean: 77.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.0061 Å20 Å27.5192 Å2
2---5.9176 Å20 Å2
3---5.9237 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.65→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 371 13 70 3007
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984175HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1284SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes412HARMONIC5
X-RAY DIFFRACTIONt_it3029HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
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_contact3303SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.86 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.266 128 4.61 %
Rwork0.2187 2648 -
all0.221 2776 -
obs--99.52 %
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)
12.2805-1.60330.07575.4231-0.0543.71780.0438-0.14950.2454-0.12390.03930.4904-0.2905-0.5566-0.08310.00350.1455-0.0416-0.09430.0941-0.0722-3.93877.219818.1935
23.25450.4773-2.05271.9305-1.23575.5942-0.0354-0.5743-0.30960.1213-0.0667-0.08710.12810.39220.1021-0.30050.0157-0.0281-0.12350.0678-0.18633.8688-3.377542.7491
32.3447-0.4888-0.77541.7101-0.40713.97280.2443-0.31650.0601-0.2164-0.3147-0.2761-0.25130.52260.0704-0.15940.02860.0278-0.04460.0778-0.018916.14360.171528.9021
41.41130.85391.13052.05252.15382.996-0.05340.2739-0.3283-0.34240.2654-0.23240.5569-0.1549-0.21190.25090.079-0.0549-0.07940.0628-0.10283.1111-10.56112.8803
50.8102-1.81690.360201.68080.0697-0.01370.0087-0.2371-0.0642-0.05840.06050.2802-0.07640.0721-0.0491-0.06090.0157-0.03060.03130.09364.0031-11.907535.0717
61.79112.29032.58387.3693-1.27114.9450.01890.13410.003-0.07990.1179-0.2613-0.01460.1478-0.13680.15970.1125-0.0598-0.0143-0.0029-0.16650.4866-4.91537.8437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|148 - 233}A148 - 233
2X-RAY DIFFRACTION2{A|234 - 382}A234 - 382
3X-RAY DIFFRACTION3{A|401 - 510}A401 - 510
4X-RAY DIFFRACTION4{T|1 - 8}T1 - 8
5X-RAY DIFFRACTION5{U|1 - 6}U1 - 6
6X-RAY DIFFRACTION6{D|1 - 6}D1 - 6

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