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- PDB-7rdt: Structure of human NTHL1 - linker 1 chimera -

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Basic information

Entry
Database: PDB / ID: 7rdt
TitleStructure of human NTHL1 - linker 1 chimera
ComponentsIsoform 3 of Endonuclease III-like protein 1
KeywordsHYDROLASE / Lyase / DNA Glycosylase
Function / homologyHydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) lyase / IRON/SULFUR CLUSTER / Isoform 3 of Endonuclease III-like protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCarroll, B.L. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA098993 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Caught in motion: human NTHL1 undergoes interdomain rearrangement necessary for catalysis.
Authors: Carroll, B.L. / Zahn, K.E. / Hanley, J.P. / Wallace, S.S. / Dragon, J.A. / Doublie, S.
History
DepositionJul 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Endonuclease III-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2822
Polymers27,9301
Non-polymers3521
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.370, 71.680, 86.520
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 Isoform 3 of Endonuclease III-like protein 1 / hNTH1 / Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase / DNA glycosylase/AP lyase


Mass: 27930.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTHL1, NTH1, OCTS3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78549-3, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: PEG 6K, Sodium chloride, Tricine,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→38.05 Å / Num. obs: 28900 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.053 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1269 / CC1/2: 0.843 / Rpim(I) all: 0.21 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RDS

7rds


Resolution: 2.1→38.05 Å / SU ML: 0.237 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 22.0233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 2889 10 %
Rwork0.1812 26011 -
obs0.1861 28900 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 8 199 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181741
X-RAY DIFFRACTIONf_angle_d0.47122373
X-RAY DIFFRACTIONf_chiral_restr0.0351270
X-RAY DIFFRACTIONf_plane_restr0.0047298
X-RAY DIFFRACTIONf_dihedral_angle_d12.9667648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.26221290.24391207X-RAY DIFFRACTION94.22
2.13-2.170.29061330.22851222X-RAY DIFFRACTION98.05
2.17-2.210.26981420.22111266X-RAY DIFFRACTION98.95
2.21-2.250.24981360.221253X-RAY DIFFRACTION98.44
2.25-2.30.25661430.21661235X-RAY DIFFRACTION97.73
2.3-2.350.28581350.20581258X-RAY DIFFRACTION97.55
2.35-2.40.2771380.22041221X-RAY DIFFRACTION95.91
2.4-2.460.26851390.20311227X-RAY DIFFRACTION95.19
2.46-2.530.25521380.20781200X-RAY DIFFRACTION95.71
2.53-2.60.24411370.19921283X-RAY DIFFRACTION98.95
2.61-2.690.27061410.18961231X-RAY DIFFRACTION98.63
2.69-2.790.2361410.19961262X-RAY DIFFRACTION98.39
2.79-2.90.23151320.1951201X-RAY DIFFRACTION96.32
2.9-3.030.27461400.19741248X-RAY DIFFRACTION95.99
3.03-3.190.26951360.18631231X-RAY DIFFRACTION97.09
3.19-3.390.25171350.16971246X-RAY DIFFRACTION99.35
3.39-3.650.19971440.1681253X-RAY DIFFRACTION97.97
3.65-4.020.17121270.15191242X-RAY DIFFRACTION95.87
4.02-4.60.19021420.1441238X-RAY DIFFRACTION98.43
4.6-5.780.21711340.15521238X-RAY DIFFRACTION97.17
5.79-38.050.18191470.15291249X-RAY DIFFRACTION97.9

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