[English] 日本語
Yorodumi
- PDB-6tur: human XPG, Apo1 form -

+
Open data


ID or keywords:

Loading...

-
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 / transcription-coupled nucleotide-excision repair / response to UV / enzyme activator activity / DNA endonuclease activity / nucleotide-excision repair ...nucleotide-excision repair complex / base-excision repair, AP site formation / bubble DNA binding / response to UV-C / RNA polymerase II complex binding / transcription-coupled nucleotide-excision repair / response to UV / enzyme activator activity / DNA endonuclease activity / nucleotide-excision repair / 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 / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / nucleoplasm / nucleus / metal ion binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more