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- PDB-6grd: eukaryotic junction-resolving enzyme GEN-1 binding with Cesium -

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Basic information

Entry
Database: PDB / ID: 6grd
Titleeukaryotic junction-resolving enzyme GEN-1 binding with Cesium
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 / Cesium
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 / Resolution: 2.66 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

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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)68,7735
Polymers68,6163
Non-polymers1572
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-77 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.390, 97.390, 119.000
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: 59156.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (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-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop
Details: PEG10000, NaCl, magnesium chloride, cesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.66→68.812 Å / Num. obs: 19265 / % possible obs: 99.9 % / Redundancy: 19.7 % / Net I/σ(I): 15
Reflection shellResolution: 2.66→2.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHASESphasing
RefinementResolution: 2.66→68.812 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.2624 1841 5.08 %
Rwork0.2444 --
obs0.2454 19229 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.47 Å2 / Biso mean: 77.3795 Å2 / Biso min: 49.61 Å2
Refinement stepCycle: final / Resolution: 2.66→68.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 595 0 0 3679
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123830
X-RAY DIFFRACTIONf_angle_d1.3075330
X-RAY DIFFRACTIONf_chiral_restr0.068600
X-RAY DIFFRACTIONf_plane_restr0.007592
X-RAY DIFFRACTIONf_dihedral_angle_d26.2151425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6604-2.73230.45781480.385926492797
2.7323-2.81270.3681620.369326372799
2.8127-2.90350.39311340.351226702804
2.9035-3.00720.40251500.323426292779
3.0072-3.12770.37281000.304427142814
3.1277-3.270.34571480.293326032751
3.27-3.44240.31340.285426522786
3.4424-3.65810.26621520.255426372789
3.6581-3.94050.25751500.235526622812
3.9405-4.3370.2241360.212926092745
4.337-4.96440.221380.226872825
4.9644-6.25390.24541460.231226262772
6.2539-68.83450.21351430.208926512794

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