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- PDB-6tt5: Crystal structure of DCLRE1C/Artemis -

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Basic information

Entry
Database: PDB / ID: 6tt5
TitleCrystal structure of DCLRE1C/Artemis
ComponentsProtein artemis
KeywordsHYDROLASE / Endonuclease / DNA repair / V(D)J recombination / NHEJ recombination
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) ...single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / endonuclease activity / adaptive immune response / damaged DNA binding / Hydrolases; Acting on ester bonds / Golgi apparatus / nucleoplasm
Similarity search - Function
DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
NICKEL (II) ION / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYosaatmadja, Y. / Goubin, S. / Newman, J.A. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
Authors: Yosaatmadja, Y. / Baddock, H.T. / Newman, J.A. / Bielinski, M. / Gavard, A.E. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Schofield, C.J. / McHugh, P.J. / Gileadi, O.
History
DepositionDec 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Protein artemis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,33510
Polymers41,7731
Non-polymers5629
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-32 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.871, 47.993, 48.246
Angle α, β, γ (deg.)82.607, 76.370, 85.983
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein artemis / DNA cross-link repair 1C protein / Protein A-SCID / SNM1 homolog C / hSNM1C / SNM1-like protein


Mass: 41773.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1C, ARTEMIS, ASCID, SCIDA, SNM1C / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 0.3 M Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→47.554 Å / Num. obs: 46964 / % possible obs: 94.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1593 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AHO

5aho


Resolution: 1.5→47.554 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.167 / Average fsc free: 0.9471 / Average fsc work: 0.9561 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1918 2199 4.684 %
Rwork0.1658 44746 -
all0.167 --
obs-46945 94.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.672 Å2-0.596 Å21.091 Å2
2--0.155 Å2-0.3 Å2
3---0.776 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 0 27 224 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133043
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172852
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6524165
X-RAY DIFFRACTIONr_angle_other_deg2.2671.5686608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90519.763169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38715523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2581531
X-RAY DIFFRACTIONr_chiral_restr0.0560.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02704
X-RAY DIFFRACTIONr_nbd_refined0.1890.2557
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.22563
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21377
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2183
X-RAY DIFFRACTIONr_metal_ion_refined0.020.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.223
X-RAY DIFFRACTIONr_nbd_other0.2040.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0820.221
X-RAY DIFFRACTIONr_mcbond_it0.8811.6411455
X-RAY DIFFRACTIONr_mcbond_other0.8781.641454
X-RAY DIFFRACTIONr_mcangle_it1.2412.4571831
X-RAY DIFFRACTIONr_mcangle_other1.2422.4591832
X-RAY DIFFRACTIONr_scbond_it0.9681.7881588
X-RAY DIFFRACTIONr_scbond_other0.9781.791589
X-RAY DIFFRACTIONr_scangle_it1.2232.612306
X-RAY DIFFRACTIONr_scangle_other1.2222.6122307
X-RAY DIFFRACTIONr_lrange_it2.42619.3223371
X-RAY DIFFRACTIONr_lrange_other1.95819.0793331
X-RAY DIFFRACTIONr_rigid_bond_restr17.73335895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2831360.20424300.20836460.8930.91370.37850.186
1.539-1.5810.211520.19631150.19735520.9360.93891.97630.177
1.581-1.6270.2051660.17731740.17935260.9410.94994.72490.161
1.627-1.6770.2221580.16230440.16533510.9460.95595.55360.149
1.677-1.7320.2061350.1629870.16232690.9470.96195.50320.147
1.732-1.7920.1921480.15829220.15931970.9470.95996.02750.146
1.792-1.860.1641220.1528180.15130460.9640.96296.520.14
1.86-1.9360.1791320.14727080.14929470.9530.96896.36920.14
1.936-2.0220.1791170.14826210.1528290.9570.96896.78330.143
2.022-2.120.191160.15825180.15927110.9510.96197.15970.153
2.12-2.2350.1891020.15623460.15725190.9470.96897.18140.154
2.235-2.370.1751210.16122570.16224360.9640.96497.6190.161
2.37-2.5330.1781100.15921360.1622920.960.96497.9930.159
2.533-2.7350.199900.16819730.1721050.9510.95598.00480.17
2.735-2.9960.213960.16718520.16919770.9470.95698.53310.172
2.996-3.3470.195830.17416400.17517460.9530.9698.68270.181
3.347-3.8620.207690.17314650.17415510.9450.95498.90390.186
3.862-4.7220.163700.14612440.14713250.9630.96499.16980.163
4.722-6.6460.208430.2049680.20410180.9450.95399.31240.224
6.646-47.5540.164330.1965270.1945720.9630.9697.90210.219

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