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- PDB-8tjg: Structure of Nei2 from Mycobacterium smegmatis in complex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 8tjg
TitleStructure of Nei2 from Mycobacterium smegmatis in complex with Zn2+
ComponentsDNA-(apurinic or apyrimidinic site) lyaseDNA-(apurinic or apyrimidinic site) lyase
KeywordsHYDROLASE / Nei2 / Nei / DNA glycosylase / AP LYASE / ENDONUCLEASE VIII / Mycobacterium smegmatis / Zn2+
Function / homology
Function and homology information


DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Nei2, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal ...Nei2, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
DNA-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWarren, G. / Shuman, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Citation
Journal: To Be Published
Title: Structure of Nei2 from Mycobacterium smegmatis in complex with Zn2+
Authors: Warren, G. / Shuman, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9562
Polymers28,8911
Non-polymers651
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.065, 57.177, 66.287
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-(apurinic or apyrimidinic site) lyase / DNA-(apurinic or apyrimidinic site) lyase


Mass: 28891.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: nei / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7G4T3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1.77 Å3/Da / Density % sol: 30.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M Bis-Tris, pH 5.5, 15% PEG-3350, cryoprotected in 100% paraffin oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→66.29 Å / Num. obs: 69151 / % possible obs: 98.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Net I/σ(I): 19.6
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1522 / CC1/2: 0.782 / Rpim(I) all: 0.305

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→43.3 Å / SU ML: 0.1307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6353
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 3196 4.62 %
Rwork0.161 65955 -
obs0.1629 69151 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 1 245 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841974
X-RAY DIFFRACTIONf_angle_d1.04212684
X-RAY DIFFRACTIONf_chiral_restr0.086303
X-RAY DIFFRACTIONf_plane_restr0.0121351
X-RAY DIFFRACTIONf_dihedral_angle_d6.017282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.28731090.23672437X-RAY DIFFRACTION82.61
1.47-1.490.28821330.22482566X-RAY DIFFRACTION89.13
1.49-1.520.29251120.21742753X-RAY DIFFRACTION94.37
1.52-1.550.25881070.19742884X-RAY DIFFRACTION96.45
1.55-1.570.19291130.18742888X-RAY DIFFRACTION98.91
1.57-1.60.19361320.16932937X-RAY DIFFRACTION99.84
1.6-1.640.22741530.1612930X-RAY DIFFRACTION100
1.64-1.670.19591170.1532891X-RAY DIFFRACTION99.97
1.67-1.710.16881510.15522944X-RAY DIFFRACTION100
1.71-1.750.23211460.16582902X-RAY DIFFRACTION100
1.75-1.80.20931500.16162899X-RAY DIFFRACTION100
1.8-1.850.2161460.15992929X-RAY DIFFRACTION100
1.85-1.910.20231200.15242920X-RAY DIFFRACTION99.9
1.91-1.980.17871650.1552904X-RAY DIFFRACTION99.97
1.98-2.060.17051240.15222924X-RAY DIFFRACTION100
2.06-2.160.17921440.1532899X-RAY DIFFRACTION100
2.16-2.270.17381540.14782931X-RAY DIFFRACTION100
2.27-2.410.15821240.15522910X-RAY DIFFRACTION100
2.41-2.60.23471420.15752937X-RAY DIFFRACTION99.94
2.6-2.860.19531910.17732866X-RAY DIFFRACTION99.84
2.86-3.270.21141820.16422866X-RAY DIFFRACTION100
3.27-4.120.19951310.14952939X-RAY DIFFRACTION100
4.13-43.30.19691500.15962899X-RAY DIFFRACTION99.87

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