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- PDB-8cg9: Crystal structure of human DNA cross-link repair 1A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8cg9
TitleCrystal structure of human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor
ComponentsDNA cross-link repair 1A protein
KeywordsHYDROLASE / DNA cross link repair / nuclease inhibition
Function / homology
Function and homology information


5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / fibrillar center / damaged DNA binding / cell division / zinc ion binding / nucleoplasm
Similarity search - Function
DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
NICKEL (II) ION / Chem-R3Z / : / DNA cross-link repair 1A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å
AuthorsNewman, J.A. / Yosaatmadja, Y. / Baddock, H.T. / Bielinski, M. / von Delft, F. / Bountra, C. / McHugh, P.J. / Schofield, C.J. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Chem Sci / Year: 2024
Title: Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target.
Authors: Bielinski, M. / Henderson, L.R. / Yosaatmadja, Y. / Swift, L.P. / Baddock, H.T. / Bowen, M.J. / Brem, J. / Jones, P.S. / McElroy, S.P. / Morrison, A. / Speake, M. / van Boeckel, S. / van ...Authors: Bielinski, M. / Henderson, L.R. / Yosaatmadja, Y. / Swift, L.P. / Baddock, H.T. / Bowen, M.J. / Brem, J. / Jones, P.S. / McElroy, S.P. / Morrison, A. / Speake, M. / van Boeckel, S. / van Doornmalen, E. / van Groningen, J. / van den Hurk, H. / Gileadi, O. / Newman, J.A. / McHugh, P.J. / Schofield, C.J.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA cross-link repair 1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0256
Polymers39,1401
Non-polymers8855
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-61 kcal/mol
Surface area14970 Å2
Unit cell
Length a, b, c (Å)51.522, 57.148, 113.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA cross-link repair 1A protein / Beta-lactamase DCLRE1A / SNM1 homolog A / hSNM1 / hSNM1A


Mass: 39140.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1A, KIAA0086, SNM1, SNM1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJP8, beta-lactamase

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Non-polymers , 6 types, 147 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-XOB / 1-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanyl-thieno[3,2-d]pyrimidine-2,4-dione


Mass: 332.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N2O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-R3Z / 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione


Mass: 332.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N2O5S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 1000, 0.1M MIB buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.68→57.19 Å / Num. obs: 39243 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.173 / Net I/σ(I): 13.6
Reflection shellResolution: 1.68→1.72 Å / Rmerge(I) obs: 8.043 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2843 / CC1/2: 0.708 / Rpim(I) all: 1.664

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.68→51.08 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2313 1895 4.84 %
Rwork0.2229 37234 -
obs0.2233 39129 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 1.68→51.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 53 142 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352680
X-RAY DIFFRACTIONf_angle_d0.63853661
X-RAY DIFFRACTIONf_chiral_restr0.0455413
X-RAY DIFFRACTIONf_plane_restr0.0049455
X-RAY DIFFRACTIONf_dihedral_angle_d17.5449959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.31571200.32372599X-RAY DIFFRACTION98.91
1.72-1.770.35471370.29912605X-RAY DIFFRACTION99.67
1.77-1.820.32961350.29282605X-RAY DIFFRACTION99.71
1.82-1.880.31791310.28822636X-RAY DIFFRACTION99.6
1.88-1.950.32861270.28522615X-RAY DIFFRACTION99.82
1.95-2.020.2711190.25482679X-RAY DIFFRACTION99.93
2.02-2.120.28141450.2482608X-RAY DIFFRACTION99.93
2.12-2.230.2551430.24622644X-RAY DIFFRACTION99.93
2.23-2.370.26011420.23542634X-RAY DIFFRACTION100
2.37-2.550.22011140.22952681X-RAY DIFFRACTION99.96
2.55-2.810.27481420.23642652X-RAY DIFFRACTION100
2.81-3.210.22331380.22332726X-RAY DIFFRACTION100
3.21-4.050.18481420.19292714X-RAY DIFFRACTION100
4.05-51.080.20261600.19262836X-RAY DIFFRACTION100

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