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- PDB-6tus: human XPG, Apo2 form -

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Basic information

Entry
Database: PDB / ID: 6tus
Titlehuman XPG, Apo2 form
Components(DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells) x 2
KeywordsDNA BINDING PROTEIN / XPG nuclease domain
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 excision repair protein ERCC-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,40710
Polymers81,6512
Non-polymers7578
Water97354
1
A: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2415
Polymers40,8611
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1665
Polymers40,7901
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.225, 134.225, 110.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#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: 40860.965 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: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 100 mM Bis-Tris pH 6.5, 200 mM Amm. Sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→47.85 Å / Num. obs: 35554 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 72.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 3887 / CC1/2: 0.439

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Processing

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

6tur


Resolution: 2.5→47.85 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 888 2.5 %
Rwork0.2029 34605 -
obs0.2038 35493 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.81 Å2 / Biso mean: 82.0475 Å2 / Biso min: 43.61 Å2
Refinement stepCycle: final / Resolution: 2.5→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 43 54 4823
Biso mean--115 80.43 -
Num. residues----583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.660.35671440.30565600574499
2.66-2.860.30861460.285856885834100
2.86-3.150.3021460.256157045850100
3.15-3.610.26541470.229157515898100
3.61-4.540.1931490.180458085957100
4.54-47.850.22491560.178360546210100

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