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- PDB-6grc: eukaryotic junction-resolving enzyme GEN-1 binding with Sodium -

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Basic information

Entry
Database: PDB / ID: 6grc
Titleeukaryotic junction-resolving enzyme GEN-1 binding with Sodium
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)
Pichia kudriavzevii (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.452 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 1.3Feb 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_seq_map_depositor_info / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end

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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)68,5474
Polymers68,5223
Non-polymers241
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-31 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.430, 98.430, 119.730
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: 59062.312 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / 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.) Pichia kudriavzevii (yeast)
#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.) Pichia kudriavzevii (yeast)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / Details: PEG10000 KCl magnesium chloride HEPES buffer pH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91376 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91376 Å / Relative weight: 1
ReflectionResolution: 2.45→49.215 Å / Num. obs: 25096 / % possible obs: 99.9 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.04 / Net I/σ(I): 16.3
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 18.8 % / Rmerge(I) obs: 2.518 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2405 / CC1/2: 0.532 / Rpim(I) all: 0.609 / Rrim(I) all: 2.674 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementResolution: 2.452→49.215 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2585 1275 5.09 %
Rwork0.23 --
obs0.2315 25059 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.4 Å2 / Biso mean: 76.6308 Å2 / Biso min: 35.48 Å2
Refinement stepCycle: final / Resolution: 2.452→49.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 595 0 37 3796
Biso mean---73.79 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123909
X-RAY DIFFRACTIONf_angle_d1.4695416
X-RAY DIFFRACTIONf_chiral_restr0.077600
X-RAY DIFFRACTIONf_plane_restr0.007600
X-RAY DIFFRACTIONf_dihedral_angle_d20.4611497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4524-2.55050.35981440.36362568271299
2.5505-2.66660.31161630.325525772740100
2.6666-2.80720.3361290.290426182747100
2.8072-2.9830.34951370.285726412778100
2.983-3.21330.27271270.264326192746100
3.2133-3.53660.25391710.237826202791100
3.5366-4.04820.25341320.210526412773100
4.0482-5.09940.22191290.187727022831100
5.0994-49.22490.24181430.221327982941100
Refinement TLS params.Method: refined / Origin x: -16.7238 Å / Origin y: 24.3051 Å / Origin z: -15.602 Å
111213212223313233
T0.5057 Å2-0.008 Å2-0.0101 Å2-0.3503 Å20.0162 Å2--0.4007 Å2
L1.8376 °2-0.2891 °2-0.1643 °2-1.4059 °2-0.1881 °2--1.7817 °2
S0.035 Å °0.0632 Å °0.1067 Å °0.1994 Å °-0.0247 Å °0.2522 Å °-0.2816 Å °-0.0811 Å °0.0037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 465
2X-RAY DIFFRACTION1allD1
3X-RAY DIFFRACTION1allH16 - 30
4X-RAY DIFFRACTION1allR0 - 15
5X-RAY DIFFRACTION1allB1 - 26
6X-RAY DIFFRACTION1allB27 - 37

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