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- PDB-6grb: eukaryotic junction-resolving enzyme GEN-1 binding with Potassium -

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Basic information

Entry
Database: PDB / ID: 6grb
Titleeukaryotic junction-resolving enzyme GEN-1 binding with Potassium
Components
  • DNA (5'-D(*TP*AP*CP*CP*CP*AP*CP*CP*AP*CP*CP*GP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')
  • Nuclease-like protein
KeywordsDNA / 4-way Holiday Junction / Resolvase / DNA recombination / GEN1 / H2TH / Potassium
Function / homology
Function and homology information


crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / DNA repair / metal ion binding
Similarity search - Function
Yen1, H3TH domain / Holliday junction resolvase Gen1, C-terminal domain / Holliday junction resolvase Gen1 C-terminal domain / 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 ...Yen1, H3TH domain / Holliday junction resolvase Gen1, C-terminal domain / Holliday junction resolvase Gen1 C-terminal domain / 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 / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclease-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLilley, D.M.J. / Liu, Y. / Freeman, D.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1.
Authors: Liu, Y. / Freeman, A.D. / Declais, A.C. / Lilley, D.M.J.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Nuclease-like protein
H: DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')
R: DNA (5'-D(*TP*AP*CP*CP*CP*AP*CP*CP*AP*CP*CP*GP*CP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2435
Polymers68,1943
Non-polymers492
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-40 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.960, 97.960, 119.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nuclease-like protein


Mass: 58734.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0007290 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYN2
#2: DNA chain DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')


Mass: 4712.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*CP*CP*CP*AP*CP*CP*AP*CP*CP*GP*CP*TP*CP*A)-3')


Mass: 4748.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 280 K / Method: evaporation / Details: HEPES pH 7.0 20% PEG 10000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.4→84.84 Å / Num. obs: 26441 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 63.42 Å2 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.53 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNQ

5cnq


Resolution: 2.4→69.227 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.86
RfactorNum. reflection% reflection
Rfree0.2728 1335 5.06 %
Rwork0.2465 --
obs0.2479 26393 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.54 Å2 / Biso mean: 76.1223 Å2 / Biso min: 45.69 Å2
Refinement stepCycle: final / Resolution: 2.4→69.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 595 2 8 3575
Biso mean--70.46 60.96 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093713
X-RAY DIFFRACTIONf_angle_d1.15177
X-RAY DIFFRACTIONf_chiral_restr0.058592
X-RAY DIFFRACTIONf_plane_restr0.008567
X-RAY DIFFRACTIONf_dihedral_angle_d24.4521361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.48580.37811290.360124582587100
2.4858-2.58530.36811170.350124822599100
2.5853-2.7030.36861410.34124722613100
2.703-2.84550.33791250.316225042629100
2.8455-3.02380.33911350.299424752610100
3.0238-3.25720.29871440.273724682612100
3.2572-3.5850.27111150.243625432658100
3.585-4.10370.23421430.2312508265199
4.1037-5.170.24731390.20682520265999
5.17-69.25540.25771470.22722628277599
Refinement TLS params.Method: refined / Origin x: 16.7412 Å / Origin y: -24.4044 Å / Origin z: -15.5058 Å
111213212223313233
T0.5262 Å2-0.0207 Å20.0349 Å2-0.3653 Å20.0096 Å2--0.3966 Å2
L1.99 °2-0.1064 °20.3581 °2-1.3406 °20.5072 °2--1.8029 °2
S0.1199 Å °0.0042 Å °-0.1252 Å °0.1799 Å °-0.0403 Å °-0.268 Å °0.2986 Å °0.0676 Å °-0.0705 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 465
2X-RAY DIFFRACTION1allH16 - 30
3X-RAY DIFFRACTION1allR0 - 15
4X-RAY DIFFRACTION1allB1 - 2
5X-RAY DIFFRACTION1allC1 - 8

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