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- PDB-6tur: human XPG, Apo1 form -

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Basic information

Entry
Database: PDB / ID: 6tur
Titlehuman XPG, Apo1 form
ComponentsDNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
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 / SAD / Resolution: 2.9 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
BBB: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
CCC: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells
DDD: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells


Theoretical massNumber of molelcules
Total (without water)163,9104
Polymers163,9104
Non-polymers00
Water00
1
AAA: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells


Theoretical massNumber of molelcules
Total (without water)40,9771
Polymers40,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells


Theoretical massNumber of molelcules
Total (without water)40,9771
Polymers40,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells


Theoretical massNumber of molelcules
Total (without water)40,9771
Polymers40,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: DNA repair protein complementing XP-G cells,DNA repair protein complementing XP-G cells


Theoretical massNumber of molelcules
Total (without water)40,9771
Polymers40,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.240, 89.560, 268.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains AAA CCC
33Chains AAA DDD
44Chains BBB CCC
55Chains BBB DDD
66Chains CCC DDD

NCS ensembles :
ID
6
1
2
3
4
5

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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: 40977.465 Da / Num. of mol.: 4
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
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 100 mM Citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→134.475 Å / Num. obs: 42886 / % possible obs: 100 % / Redundancy: 80 % / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→3.01 Å / Num. unique obs: 4403 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→67.6 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU B: 25.688 / SU ML: 0.433 / Cross valid method: FREE R-VALUE / ESU R: 2.713 / ESU R Free: 0.408
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2814 1071 2.501 %
Rwork0.2375 41757 -
all0.239 --
obs-42828 99.995 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 101.744 Å2
Baniso -1Baniso -2Baniso -3
1--5.093 Å2-0 Å20 Å2
2--6.335 Å2-0 Å2
3----1.242 Å2
Refinement stepCycle: LAST / Resolution: 2.9→67.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10271 0 0 0 10271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179954
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.64414214
X-RAY DIFFRACTIONr_angle_other_deg1.1551.57723101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91451251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26122.522559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.511151828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7771563
X-RAY DIFFRACTIONr_chiral_restr0.0710.21314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022246
X-RAY DIFFRACTIONr_nbd_refined0.2240.22059
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.29161
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24850
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2152
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.240
X-RAY DIFFRACTIONr_nbd_other0.2770.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3040.21
X-RAY DIFFRACTIONr_mcbond_it9.92810.635052
X-RAY DIFFRACTIONr_mcbond_other9.91210.6295051
X-RAY DIFFRACTIONr_mcangle_it14.75715.9066287
X-RAY DIFFRACTIONr_mcangle_other14.75615.9076288
X-RAY DIFFRACTIONr_scbond_it9.50611.055463
X-RAY DIFFRACTIONr_scbond_other9.50511.0515464
X-RAY DIFFRACTIONr_scangle_it14.64116.3237927
X-RAY DIFFRACTIONr_scangle_other14.6416.3247928
X-RAY DIFFRACTIONr_lrange_it18.764118.41911297
X-RAY DIFFRACTIONr_lrange_other18.763118.42711298
X-RAY DIFFRACTIONr_ncsr_local_group_10.1430.059088
X-RAY DIFFRACTIONr_ncsr_local_group_20.1390.058951
X-RAY DIFFRACTIONr_ncsr_local_group_30.1480.059286
X-RAY DIFFRACTIONr_ncsr_local_group_40.1270.059343
X-RAY DIFFRACTIONr_ncsr_local_group_50.1480.059126
X-RAY DIFFRACTIONr_ncsr_local_group_60.1440.058995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.9-2.9750.394770.39630150.39630920.6860.7321000.396
2.975-3.0570.395760.3929720.3930480.590.6031000.39
3.057-3.1450.371750.37628860.37529610.590.5921000.376
3.145-3.2420.324710.34327770.34228490.6630.68299.96490.343
3.242-3.3480.361690.3127190.31127880.7540.7941000.31
3.348-3.4660.354680.29726570.29827250.7490.8061000.297
3.466-3.5970.348660.28825520.28926180.7980.8291000.288
3.597-3.7430.287630.24324650.24425280.8470.8941000.243
3.743-3.910.262610.24323520.24424130.880.8941000.243
3.91-4.10.316580.24922730.2523310.8550.8811000.249
4.1-4.3220.261550.21121400.21221950.9080.9251000.211
4.322-4.5840.225520.18120410.18220930.9270.941000.181
4.584-4.90.243500.17619330.17719830.920.9421000.176
4.9-5.2920.249450.18817940.1918390.9310.9411000.188
5.292-5.7960.257430.19816540.216970.9360.9441000.198
5.796-6.4790.307390.20615370.20915760.9160.9461000.206
6.479-7.4780.273350.21313570.21413920.9160.9341000.213
7.478-9.1520.22300.1611540.16211840.9490.961000.16
9.152-12.9130.22230.1739300.1749530.9370.9671000.173
12.913-134.4750.331150.4465490.4435650.880.85799.8230.446

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