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- PDB-8cf0: Crystal structure of human DNA cross-link repair 1A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8cf0
TitleCrystal structure of human DNA cross-link repair 1A in complex with quinoxalinedione inhibitor H2
ComponentsDNA cross-link repair 1A protein
KeywordsHYDROLASE / SNM1A / nuclease inhibitor / ICL
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 / : / DNA cross-link repair 1A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 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 2, 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)39,5254
Polymers39,1401
Non-polymers3843
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint0 kcal/mol
Surface area15580 Å2
Unit cell
Length a, b, c (Å)51.313, 56.209, 112.951
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

#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
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-UF3 / 9-chloranyl-1,4-dihydropyrazino[2,3-c]quinoline-2,3-dione


Mass: 247.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H6ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 249 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 298 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→56.48 Å / Num. obs: 33172 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.052 / Net I/σ(I): 7.3
Reflection shellResolution: 1.76→1.81 Å / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2402 / CC1/2: 0.489

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→56.48 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2567 1646 5.1 %
Rwork0.2196 30630 -
obs0.2214 32276 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.11 Å2
Refinement stepCycle: LAST / Resolution: 1.76→56.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 22 249 2963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232828
X-RAY DIFFRACTIONf_angle_d0.54253854
X-RAY DIFFRACTIONf_chiral_restr0.044427
X-RAY DIFFRACTIONf_plane_restr0.0039485
X-RAY DIFFRACTIONf_dihedral_angle_d19.13481022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.37791320.3882340X-RAY DIFFRACTION90.88
1.81-1.870.34441250.35742440X-RAY DIFFRACTION94.72
1.87-1.940.3651270.32492463X-RAY DIFFRACTION94.94
1.94-2.010.32041170.2872546X-RAY DIFFRACTION97.37
2.01-2.110.29521380.25162513X-RAY DIFFRACTION97.5
2.11-2.220.2581460.23992537X-RAY DIFFRACTION97.56
2.22-2.360.29381440.21992551X-RAY DIFFRACTION97.89
2.36-2.540.27491420.22092567X-RAY DIFFRACTION98.58
2.54-2.790.23721340.21912595X-RAY DIFFRACTION98.91
2.79-3.20.22661510.21892606X-RAY DIFFRACTION99.03
3.2-4.030.22681450.1842670X-RAY DIFFRACTION99.4
4.03-56.480.23271450.1872802X-RAY DIFFRACTION99.7

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