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- PDB-5d4b: Structural Basis for a New Templated Activity by Terminal Deoxynu... -

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Basic information

Entry
Database: PDB / ID: 5d4b
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*C)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-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 / DNA repair / chromatin / 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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / 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
DNA / DNA nucleotidylexotransferase / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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: Terminal deoxynucleotidyltransferase
C: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
E: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,83618
Polymers98,9736
Non-polymers86312
Water2,792155
1
A: Terminal deoxynucleotidyltransferase
C: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
E: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89010
Polymers51,4594
Non-polymers4326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terminal deoxynucleotidyltransferase
D: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
E: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89010
Polymers51,4594
Non-polymers4326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.730, 71.450, 198.170
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 , 1 types, 2 molecules AB

#1: Protein Terminal deoxynucleotidyltransferase


Mass: 45704.008 Da / Num. of mol.: 2
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 CDEF

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


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


Mass: 2134.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 167 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.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
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: Jun 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.66→49.23 Å / Num. all: 23888 / Num. obs: 22902 / % possible obs: 95.9 % / Redundancy: 5 % / Biso Wilson estimate: 83.28 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.114 / Net I/σ(I): 11.47
Reflection shellResolution: 2.66→2.83 Å / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.67 / % possible all: 90.5

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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: 2.66→49.23 Å / Cor.coef. Fo:Fc: 0.9367 / Cor.coef. Fo:Fc free: 0.9098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1153 5 %RANDOM
Rwork0.2072 ---
obs0.2091 22902 96.34 %-
Displacement parametersBiso mean: 67.34 Å2
Baniso -1Baniso -2Baniso -3
1-10.3425 Å20 Å20 Å2
2---2.7688 Å20 Å2
3----7.5737 Å2
Refine analyzeLuzzati coordinate error obs: 0.373 Å
Refinement stepCycle: 1 / Resolution: 2.66→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 484 44 155 5871
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015868HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.068049HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1849SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes828HARMONIC5
X-RAY DIFFRACTIONt_it5868HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion19.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion787SEMIHARMONIC5
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_contact6477SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.78 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3337 129 4.98 %
Rwork0.2532 2461 -
all0.2571 2590 -
obs--96.34 %
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)
10.2892-0.0272-0.17890.32840.2931.3780.00680.02090.0519-0.0165-0.0090.0451-0.03120.03730.0022-0.0556-0.0146-0.0077-0.0748-0.00160.018832.09217.0541-26.1692
20.29140.04650.01830.566-0.52691.75020.0369-0.0682-0.0428-0.0602-0.2006-0.0339-0.0027-0.0160.1637-0.07730.03220.009-0.0718-0.0068-0.02131.8273-7.324725.3918
30.04690.0013-0.14550.0041-0.09760.13160-0.001-0.00780.00180.00110.00170.008-0.0029-0.00110.00710.02040.0159-0.0055-0.00250.004533.3667-5.1571-29.3393
40.119-0.0425-0.19720.0798-0.01290-0.00080.00890.0049-0.0014-0.0051-0.0022-0.0080.00480.00590.0029-0.01250.0045-0.01380.00140.021935.25714.675728.3852
50.1340.038-0.08330.15120.08250.1241-0.00030.00290.0006-0.00430.00130.01110.0014-0.0022-0.0010.0057-0.0001-0.0110.00310.00330.001938.3817-4.2953-1.0657
60-0.2938-0.47960.33850.067300.0005-0.0007-0.0001-0.00160.00250.0084-0.002-0.0006-0.00290.02160.00480.0417-0.0060.02560.002137.34042.30433.683
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|* }
6X-RAY DIFFRACTION6{ F|* }

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