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- PDB-5d46: Structural Basis for a New Templated Activity by Terminal Deoxynu... -

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Basic information

Entry
Database: PDB / ID: 5d46
TitleStructural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3')
  • Terminal deoxynucleotidyltransferase
KeywordsTRANSFERASE / Tdt / Synapsis / Double strand breaks
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 / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / 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 / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / 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
ACETATE ION / PYROPHOSPHATE 2- / DNA / DNA nucleotidylexotransferase / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLoc'h, J. / Rosario, S. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARC pour la recherche sur le cancer France
CitationJournal: Structure / Year: 2016
Title: Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
Authors: Loc'h, J. / Rosario, S. / Delarue, M.
History
DepositionAug 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terminal deoxynucleotidyltransferase
B: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
C: DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3')
D: DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3')
E: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,10613
Polymers53,5135
Non-polymers5938
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-66 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.980, 75.000, 125.910
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-787-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Terminal deoxynucleotidyltransferase


Mass: 45704.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UZ80, UniProt: P09838*PLUS

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DNA chain , 2 types, 4 molecules BECD

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


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


Mass: 2094.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 112 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22-28% PEG 4000, 100-300 mM Lithium Sulfate and 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→44.57 Å / Num. all: 12844 / Num. obs: 12647 / % possible obs: 98.5 % / Redundancy: 3 % / Biso Wilson estimate: 106.35 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.07 / Net I/σ(I): 12.67
Reflection shellResolution: 2.8→2.97 Å / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.75 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JMS

1jms


Resolution: 2.8→44.57 Å / Cor.coef. Fo:Fc: 0.9249 / Cor.coef. Fo:Fc free: 0.9014 / SU R Cruickshank DPI: 2.051 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 6.066 / SU Rfree Blow DPI: 0.338 / SU Rfree Cruickshank DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 633 5.01 %RANDOM
Rwork0.1976 ---
obs0.2 12645 98.55 %-
Displacement parametersBiso mean: 92.69 Å2
Baniso -1Baniso -2Baniso -3
1--19.7549 Å20 Å2-9.9582 Å2
2--19.064 Å20 Å2
3---0.6909 Å2
Refine analyzeLuzzati coordinate error obs: 0.483 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 485 33 104 3105
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013094HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064286HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d928SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it3094HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion19.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion411SEMIHARMONIC5
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_contact3350SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3403 149 5 %
Rwork0.2638 2832 -
all0.2674 2981 -
obs--98.55 %
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)
13.58911.28881.61854.8481.54193.29020.5161-0.1152-0.25220.7778-0.47490.11390.2458-0.0062-0.0412-0.2335-0.04360.0599-0.2574-0.0197-0.246757.23181.610933.3441
20.6771-0.7947-0.69772.60070.18320.48620.0013-0.09740.03290.0425-0.0094-0.0308-0.04570.020.00820.1151-0.2567-0.0573-0.1936-0.14940.220257.077721.661638.9867
31.70520.53551.92130.60120.40950.51410.00610.03690.107-0.0402-0.0029-0.0069-0.08670.0072-0.00320.0203-0.10990.0924-0.1372-0.03740.198960.034515.685833.6688
4-0.601-2.9391.91193.0819-0.15322.6841-0.02940.12880.143-0.2080.08570.2006-0.16890.017-0.05630.24410.0947-0.07420.0976-0.0892-0.240956.14569.564512.694
51.0071.2129-1.71351.2891-0.61432.9125-0.00640.034-0.0629-0.01540.03870.0620.0027-0.0131-0.03220.04980.1517-0.05380.1984-0.0519-0.165157.40723.07378.343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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