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- PDB-5cnq: Crystal structure of the Holliday junction-resolving enzyme GEN1 ... -

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Basic information

Entry
Database: PDB / ID: 5cnq
TitleCrystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA, Mg2+ and Mn2+ ions
Components
  • DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')
  • Nuclease-like protein
  • R
KeywordsREPLICATION / GEN1 / 4-way Holiday junction / resolvase / DNA damage repair
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)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsLiu, Y.J. / Freeman, A.D.J. / Declais, A.C. / Wilson, T.J. / Gartner, A. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Cell Rep / Year: 2015
Title: Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.
Authors: Liu, Y. / Freeman, A.D. / Declais, A.C. / Wilson, T.J. / Gartner, A. / Lilley, D.M.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclease-like protein
R: R
H: DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5825
Polymers61,4723
Non-polymers1102
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-35 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.582, 98.582, 119.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nuclease-like protein


Mass: 52012.102 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 2-465
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 R


Mass: 4748.097 Da / Num. of mol.: 1 / Fragment: R-stem / Source method: obtained synthetically / Details: DNA oligo synthesis / Source: (synth.) Escherichia coli (E. coli)
#3: 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.) Escherichia coli (E. coli)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.73 Å3/Da / Density % sol: 54.99 % / Description: cube
Crystal growTemperature: 279 K / Method: evaporation / pH: 7 / Details: PEG10000, NaCl, magnesium chloride / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN protection
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: 2.6→49.291 Å / Num. obs: 21142 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 19.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 15 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
PHENIX1.9-1692phasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO8

5co8


Resolution: 2.602→49.291 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1084 5.13 %Random selection
Rwork0.212 ---
obs0.214 21111 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.602→49.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 595 2 66 3734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053805
X-RAY DIFFRACTIONf_angle_d0.8745272
X-RAY DIFFRACTIONf_dihedral_angle_d19.6921457
X-RAY DIFFRACTIONf_chiral_restr0.034584
X-RAY DIFFRACTIONf_plane_restr0.006580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.602-2.72040.37381440.31332455X-RAY DIFFRACTION100
2.7204-2.86380.33741560.29322425X-RAY DIFFRACTION100
2.8638-3.04320.30971380.2652474X-RAY DIFFRACTION100
3.0432-3.27810.27911380.24412469X-RAY DIFFRACTION100
3.2781-3.60790.28631190.22142506X-RAY DIFFRACTION100
3.6079-4.12980.23711330.18312505X-RAY DIFFRACTION100
4.1298-5.20220.1761160.18182553X-RAY DIFFRACTION100
5.2022-49.29980.25481400.20792640X-RAY DIFFRACTION100

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