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- PDB-6tux: human XPG-DNA, Complex 2 -

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Basic information

Entry
Database: PDB / ID: 6tux
Titlehuman XPG-DNA, Complex 2
Components
  • DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')
  • DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
KeywordsDNA BINDING PROTEIN / XPG nuclease domain bound to DNA
Function / homology
Function and homology information


nucleotide-excision repair complex / base-excision repair, AP site formation / bubble DNA binding / response to UV-C / RNA polymerase II complex binding / response to UV / transcription-coupled nucleotide-excision repair / DNA endonuclease activity / nucleotide-excision repair / enzyme activator activity ...nucleotide-excision repair complex / base-excision repair, AP site formation / bubble DNA binding / response to UV-C / RNA polymerase II complex binding / response to UV / transcription-coupled nucleotide-excision repair / DNA endonuclease activity / nucleotide-excision repair / enzyme activator activity / double-strand break repair via homologous recombination / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / single-stranded DNA binding / chromosome / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / protein-containing complex / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA excision repair protein ERCC-5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRuiz, F.M. / Fernandez-Tornero, C.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair.
Authors: Gonzalez-Corrochano, R. / Ruiz, F.M. / Taylor, N.M.I. / Huecas, S. / Drakulic, S. / Spinola-Amilibia, M. / Fernandez-Tornero, C.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
B: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
C: DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')
D: DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')
E: DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)94,0546
Polymers94,0546
Non-polymers00
Water00
1
A: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
C: DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')
D: DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)47,0273
Polymers47,0273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
E: DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)47,0273
Polymers47,0273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.650, 127.650, 118.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells / DNA excision repair protein ERCC-5 / Xeroderma pigmentosum group G-complementing protein


Mass: 40304.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC5, ERCM2, XPG, XPGC / Production host: Escherichia coli (E. coli)
References: UniProt: P28715, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*GP*CP*AP*GP*AP*GP*TP*T)-3')


Mass: 3364.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*CP*TP*CP*TP*GP*C)-3')


Mass: 3358.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 5% PEG 3350, 50 mM Na Citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→49.67 Å / Num. obs: 18419 / % possible obs: 99.9 % / Redundancy: 27.4 % / Biso Wilson estimate: 117.07 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.9
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 3269 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TUR

6tur


Resolution: 3.1→49.67 Å / SU ML: 0.403 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3027 551 3.01 %
Rwork0.247 17753 -
obs0.2487 18304 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 145.28 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5245 615 0 0 5860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266055
X-RAY DIFFRACTIONf_angle_d0.55998306
X-RAY DIFFRACTIONf_chiral_restr0.0402908
X-RAY DIFFRACTIONf_plane_restr0.005960
X-RAY DIFFRACTIONf_dihedral_angle_d25.14792297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.410.41781390.3684292X-RAY DIFFRACTION98.47
3.41-3.910.35991300.28624382X-RAY DIFFRACTION99.58
3.91-4.920.26511340.2324441X-RAY DIFFRACTION99.78
4.92-49.670.2921480.22884638X-RAY DIFFRACTION99.5

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