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- PDB-4iqw: Tdt core in complex with inhibitor (2Z,5E)-6-[4-(4-fluorobenzoyl)... -

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Basic information

Entry
Database: PDB / ID: 4iqw
TitleTdt core in complex with inhibitor (2Z,5E)-6-[4-(4-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 / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb 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 / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb 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 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
Chem-1FQ / DNA / DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)45,1734
Polymers44,8212
Non-polymers3522
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.650, 84.670, 114.730
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: 43628.734 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-1FQ / (2Z,5E)-6-[4-(4-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.: 187 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG4000, 200 mM sodium formate, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING 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: 2.6→47.5 Å / Num. all: 14577 / Num. obs: 14429 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 59.25 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2089 / % 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: 2.6→47.49 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9011 / SU R Cruickshank DPI: 0.594 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.858 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.275 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 732 5.07 %RANDOM
Rwork0.1881 ---
obs0.1901 14428 99 %-
Displacement parametersBiso mean: 56.11 Å2
Baniso -1Baniso -2Baniso -3
1-6.3175 Å20 Å20 Å2
2--4.2283 Å20 Å2
3----10.5458 Å2
Refine analyzeLuzzati coordinate error obs: 0.333 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 40 25 187 3072
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012956HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes436HARMONIC5
X-RAY DIFFRACTIONt_it2956HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
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_contact3389SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.81 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2586 151 5.19 %
Rwork0.2047 2760 -
all0.2075 2911 -
obs--99 %
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)
13.63571.5989-1.16132.39961.34582.5635-0.0050.12850.1168-0.3313-0.0337-0.0888-0.25160.04050.0387-0.17390.0345-0.0021-0.14590.02460.167327.736511.46535.501
20.8420.21050.11052.1350.45960.4179-0.0241-0.12790.05810.1487-0.02820.30030.0008-0.08910.0523-0.19-0.0010.063-0.1807-0.02880.217612.029211.219329.917
34.1764-0.93391.21730-0.42170.9372-0.00540.3132-0.2098-0.0414-0.12750.22520.1347-0.08560.1329-0.17980.0094-0.0202-0.1244-0.09090.27457.4184-1.26428.6273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|149 - 238}A149 - 238
2X-RAY DIFFRACTION2{A|239 - 453}A239 - 453
3X-RAY DIFFRACTION3{A|454 - 510}A454 - 510

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