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- PDB-4i2j: Binary complex of mouse TdT with dCTP -

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Basic information

Entry
Database: PDB / ID: 4i2j
TitleBinary complex of mouse TdT with dCTP
ComponentsDNA nucleotidylexotransferase
KeywordsTRANSFERASE / Terminal transferase
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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: DNA nucleotidylexotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4336
Polymers45,7041
Non-polymers7295
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 85.250, 111.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-26% PEG4000, 100 mM HEPES, 200 mM lithium chloride, 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: ID14-4 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2003
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→19.42 Å / Num. all: 12388 / Num. obs: 12388 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 64.59 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / Num. unique all: 1300 / % possible all: 90

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Processing

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

1jms


Resolution: 2.7→19.42 Å / Cor.coef. Fo:Fc: 0.9193 / Cor.coef. Fo:Fc free: 0.8913 / SU R Cruickshank DPI: 1.215 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.326 / SU Rfree Cruickshank DPI: 0.319 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 598 4.83 %RANDOM
Rwork0.1918 ---
obs0.194 12388 96.02 %-
Displacement parametersBiso mean: 61.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.2416 Å20 Å20 Å2
2--6.4628 Å20 Å2
3----7.7044 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 32 163 2942
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012831HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.023834HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1298SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes415HARMONIC5
X-RAY DIFFRACTIONt_it2831HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
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_contact3172SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.96 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2938 142 5.1 %
Rwork0.2056 2641 -
all0.2099 2783 -
obs--96.02 %
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)
13.14372.9061.15131.477-1.110900.03420.00080.0123-0.0885-0.1152-0.0409-0.08420.00320.0809-0.21160.0140.0584-0.1075-0.00330.239648.605352.31864.1693
20.9531-0.5578-0.61263.01582.90512.2313-0.0640.17610.2455-0.28930.0117-0.1405-0.43130.03190.0523-0.2996-0.01070.0292-0.26160.07410.30451.539859.503664.5282
31.23111.29040.24663.979-0.55740.5031-0.021-0.17260.22210.1128-0.1454-0.0872-0.0641-0.37130.1665-0.20780.02760.0261-0.2723-0.08370.30442.23967.670587.3277
43.767-0.75541.28593.05850.65393.14960.1275-0.2943-0.01330.2728-0.15890.32910.0827-0.52690.0314-0.304-0.03180.1036-0.3040.02810.30432.075245.63486.0884
58.0159-0.45322.27441.9492-0.69011.2712-0.0090.2315-0.338-0.15080.00970.08270.2545-0.2285-0.0007-0.3040.0160.0188-0.2198-0.03380.30431.518941.043563.5189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|149 - 184}A149 - 184
2X-RAY DIFFRACTION2{A|185 - 263}A185 - 263
3X-RAY DIFFRACTION3{A|264 - 307}A264 - 307
4X-RAY DIFFRACTION4{A|308 - 453}A308 - 453
5X-RAY DIFFRACTION5{A|454 - 510}A454 - 510

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