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- PDB-6tuw: human XPG-DNA, Complex 1 -

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Basic information

Entry
Database: PDB / ID: 6tuw
Titlehuman XPG-DNA, Complex 1
Components
  • DNA (5'-D(P*GP*AP*AP*CP*TP*CP*TP*G)-3')
  • DNA (5'-D(P*TP*GP*CP*AP*GP*AP*GP*TP*TP*C)-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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 (5'-D(P*TP*GP*CP*AP*GP*AP*GP*TP*TP*C)-3')
C: DNA (5'-D(P*GP*AP*AP*CP*TP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)47,5123
Polymers47,5123
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.510, 129.510, 118.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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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: 40789.887 Da / Num. of mol.: 1
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*TP*GP*CP*AP*GP*AP*GP*TP*TP*C)-3')


Mass: 3364.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(P*GP*AP*AP*CP*TP*CP*TP*G)-3')


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (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: 2.62 Å3/Da / Density % sol: 53.05 %
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: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→45.79 Å / Num. obs: 6627 / % possible obs: 99.8 % / Redundancy: 15.9 % / Biso Wilson estimate: 145.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 3.5→3.625 Å / Num. unique obs: 1536 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TUR

6tur


Resolution: 3.5→45.79 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.6614
RfactorNum. reflection% reflection
Rfree0.2932 331 5.05 %
Rwork0.2652 --
obs0.2665 6548 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 212.3 Å2
Refinement stepCycle: LAST / Resolution: 3.5→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 370 0 0 2914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423017
X-RAY DIFFRACTIONf_angle_d0.68364151
X-RAY DIFFRACTIONf_chiral_restr0.044453
X-RAY DIFFRACTIONf_plane_restr0.0111476
X-RAY DIFFRACTIONf_dihedral_angle_d16.76841733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-4.410.35311620.33523031X-RAY DIFFRACTION98.46
4.41-45.790.27781690.24433186X-RAY DIFFRACTION98.76

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