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- PDB-4iqv: Tdt core in complex with inhibitor 6-[4-(3-fluorobenzoyl)-1H-pyrr... -

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Basic information

Entry
Database: PDB / ID: 4iqv
TitleTdt core in complex with inhibitor 6-[4-(3-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA
Components
  • 5'-D(*GP*CP*CP*G)-3'
  • DNA nucleotidylexotransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR/DNA / terminal transferase / TRANSFERASE-TRANSFERASE INHIBITOR-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 / 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 / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / BRCA1 C Terminus (BRCT) domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda ...DNA nucleotidylexotransferase (TdT) / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / BRCA1 C Terminus (BRCT) domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / breast cancer carboxy-terminal domain / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / 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
Chem-1FO / DNA / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: J.Med.Chem. / Year: 2013
Title: New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target.
Authors: Costi, R. / Cuzzucoli Crucitti, G. / Pescatori, L. / Messore, A. / Scipione, L. / Tortorella, S. / Amoroso, A. / Crespan, E. / Campiglia, P. / Maresca, B. / Porta, A. / Granata, I. / ...Authors: Costi, R. / Cuzzucoli Crucitti, G. / Pescatori, L. / Messore, A. / Scipione, L. / Tortorella, S. / Amoroso, A. / Crespan, E. / Campiglia, P. / Maresca, B. / Porta, A. / Granata, I. / Novellino, E. / Gouge, J. / Delarue, M. / Maga, G. / Di Santo, R.
History
DepositionJan 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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.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(*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2064
Polymers46,8542
Non-polymers3522
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.860, 84.540, 122.950
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: 45661.941 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: L398A
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(*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1FO / 6-[4-(3-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid


Mass: 329.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12FNO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% PEG4000, 200 mM ammonium formate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2012 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→49.7 Å / Num. all: 11375 / Num. obs: 11303 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 73.85 Å2 / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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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: 2.9→22.67 Å / Cor.coef. Fo:Fc: 0.9043 / Cor.coef. Fo:Fc free: 0.8817 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.384 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 538 4.77 %RANDOM
Rwork0.1793 ---
obs0.1824 11278 99.42 %-
Displacement parametersBiso mean: 53.12 Å2
Baniso -1Baniso -2Baniso -3
1-8.1549 Å20 Å20 Å2
2--15.7528 Å20 Å2
3----23.9077 Å2
Refine analyzeLuzzati coordinate error obs: 0.339 Å
Refinement stepCycle: LAST / Resolution: 2.9→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 40 25 184 3089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012966HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984008HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1392SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it2966HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion2.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion383SEMIHARMONIC5
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_contact3323SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 127 4.81 %
Rwork0.2126 2513 -
all0.2168 2640 -
obs--99.42 %
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)
12.8040.1389-0.24181.04350.9991.02880.0418-0.1002-0.0051-0.1775-0.0428-0.1782-0.2864-0.0730.001-0.07250.00530.0237-0.04810.02190.034827.332616.44097.507
21.370.84890.3442.6930.65420.59860.0016-0.11390.02940.11-0.01690.18110.004-0.10590.0153-0.16940.00290.0625-0.1291-0.02050.081511.910516.758732.7253
34.8395-0.74250.95931.5936-0.22292.12660.02760.1098-0.17370.2046-0.06620.17120.0058-0.01680.0386-0.19790.0051-0.0149-0.056-0.03170.11597.20093.820612.1774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|148 - 240}A148 - 240
2X-RAY DIFFRACTION2{A|241 - 443}A241 - 443
3X-RAY DIFFRACTION3{A|444 - 510}A444 - 510

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