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- PDB-4i2c: Ternary complex of mouse TdT with ssDNA and AMPcPP -

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Basic information

Entry
Database: PDB / ID: 4i2c
TitleTernary complex of mouse TdT with ssDNA and AMPcPP
Components
  • 5'-D(*AP*AP*AP*AP*A)-3'
  • DNA nucleotidylexotransferase
KeywordsTRANSFERASE/DNA / Terminal transferase / 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 / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase 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 / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / 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 beta thumb / DNA polymerase, thumb domain superfamily / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / : / DNA / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism.
Authors: Gouge, J. / Rosario, S. / Romain, F. / Beguin, P. / Delarue, M.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 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
C: 5'-D(*AP*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8636
Polymers47,2252
Non-polymers6384
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.875, 84.763, 116.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

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


Mass: 45704.008 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
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
#2: DNA chain 5'-D(*AP*AP*AP*AP*A)-3'


Mass: 1521.077 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 353 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN FRAGMENT IS THE CATALYTIC CORE OF THE TDT-S (TDT-SMALL) ISOFORM (UNP RESIDUES 132-482, 503-530).

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-26% PEG4000, 100 mM HEPES, 200 mM ammonium formate, pH 6.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / 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: 2.1→48 Å / Num. obs: 27460 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3993 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JMS

1jms


Resolution: 2.1→25.45 Å / Cor.coef. Fo:Fc: 0.9379 / Cor.coef. Fo:Fc free: 0.9154 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.158 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1386 5.06 %RANDOM
Rwork0.1814 ---
obs0.1832 27412 98.5 %-
Displacement parametersBiso mean: 35.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.4423 Å20 Å20 Å2
2--1.0403 Å20 Å2
3----5.4827 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 2.1→25.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 33 34 349 3289
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012975HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14014HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1397SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes459HARMONIC5
X-RAY DIFFRACTIONt_it2975HARMONIC20
X-RAY DIFFRACTIONt_nbd28SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion2.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion379SEMIHARMONIC5
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_contact3509SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2453 140 4.92 %
Rwork0.2175 2705 -
all0.2188 2845 -
obs--98.5 %
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)
12.6652-0.1213-0.17352.3216-0.34431.15810.0528-0.13980.13680.129-0.01140.0282-0.16930.0014-0.0413-0.09270.00520.0136-0.0777-0.01970.0186-27.492812.5425-6.2396
21.1247-0.5257-0.45863.37480.65581.4844-0.0596-0.0365-0.06480.14680.0445-0.07830.13550.20280.0151-0.01860.01160.0016-0.05950.03880.1618-18.527728.0866-29.1113
31.4969-0.02850.38951.3874-0.80711.297-0.04130.1490.0118-0.2156-0.0476-0.21310.07390.13130.0888-0.10620.00750.0465-0.1206-0.02270.08-8.58694.2204-31.4225
44.67040.58250.90970.1637-0.38220.21540.0756-0.3298-0.3370.0768-0.1175-0.1464-0.0145-0.01220.042-0.1168-0.011-0.0068-0.06850.03730.1176-6.9984-1.153-9.2088
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 - 302}A244 - 302
3X-RAY DIFFRACTION3{A|303 - 452}A303 - 452
4X-RAY DIFFRACTION4{A|453 - 510}A453 - 510

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