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- PDB-5u6z: Crystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain -

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Basic information

Entry
Database: PDB / ID: 5u6z
TitleCrystal Structure of Xenopus laevis Apex2 C-terminal Znf-GRF Domain
ComponentsDNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE / GRF Zinc Finger / 3' AP Endo/Exonuclease / DNA binding
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / chromosome / endonuclease activity / mitochondrion / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
DNA-(apurinic or apyrimidinic site) endonuclease 2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWallace, B.D. / Williams, R.S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress.
Authors: Wallace, B.D. / Berman, Z. / Mueller, G.A. / Lin, Y. / Chang, T. / Andres, S.N. / Wojtaszek, J.L. / DeRose, E.F. / Appel, C.D. / London, R.E. / Yan, S. / Williams, R.S.
History
DepositionDec 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,4343
Polymers8,2731
Non-polymers1612
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area5680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.332, 90.332, 23.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 8272.509 Da / Num. of mol.: 1 / Fragment: residues 446-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: apex2, apex2-prov / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DDT4, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M (NH4)2SO4, 0.1 M Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.28257 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28257 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 5570 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 56.07 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.6-2.643.20.3140.945184.4
2.64-2.693.20.2730.941191.7
2.69-2.743.20.2310.953192.6
2.74-2.83.30.2090.97195.2
2.8-2.863.50.1960.979195.9
2.86-2.933.60.1740.99197.1
2.93-33.70.1670.9811100
3-3.083.70.1690.9791100
3.08-3.173.70.1410.9891100
3.17-3.283.70.1190.9871100
3.28-3.393.80.1060.9851100
3.39-3.533.80.0870.9911100
3.53-3.693.90.0840.991100
3.69-3.883.90.0740.9921100
3.88-4.133.90.0630.9961100
4.13-4.453.90.0660.993199.6
4.45-4.893.90.0660.9931100
4.89-5.63.90.050.9951100
5.6-7.053.90.0620.9931100
7.05-503.80.0580.994199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→45.166 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.61
RfactorNum. reflection% reflection
Rfree0.2446 559 10.05 %
Rwork0.1948 --
obs0.2 5562 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.73 Å2 / Biso mean: 43.12 Å2 / Biso min: 28.97 Å2
Refinement stepCycle: final / Resolution: 2.6→45.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms519 0 6 18 543
Biso mean--62.15 42.1 -
Num. residues----67
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013542
X-RAY DIFFRACTIONf_angle_d1.46738
X-RAY DIFFRACTIONf_chiral_restr0.08273
X-RAY DIFFRACTIONf_plane_restr0.00997
X-RAY DIFFRACTIONf_dihedral_angle_d16.61200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.585-2.84510.28981360.23451164130092
2.8451-3.25670.30481380.21971271140999
3.2567-4.10260.24571370.188512901427100
4.1026-45.17290.22031480.184712781426100

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