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- PDB-5co8: Crystal structure of the Holliday junction-resolving enzyme GEN1 ... -

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Basic information

Entry
Database: PDB / ID: 5co8
TitleCrystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA and Mg2+ ion
Components
  • (Nuclease-like ...) x 2
  • DNA (31-MER)
  • DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*TP*C)-3')
  • DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*A)-3')
KeywordsHYDROLASE / Holiday junction / resolvase / Complex / DNA
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn
Revision 1.2Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: DNA (31-MER)
C: Nuclease-like protein
X: DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*TP*C)-3')
A: Nuclease-like protein
H: DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,9757
Polymers122,9275
Non-polymers492
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.072, 98.072, 119.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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DNA chain , 3 types, 3 molecules RXH

#1: DNA chain DNA (31-MER)


Mass: 9337.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*CP*TP*GP*CP*AP*GP*TP*TP*GP*AP*GP*TP*C)-3')


Mass: 4938.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*TP*GP*AP*GP*CP*GP*GP*TP*GP*GP*TP*TP*GP*GP*A)-3')


Mass: 4721.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Nuclease-like ... , 2 types, 2 molecules CA

#2: Protein Nuclease-like protein


Mass: 52012.102 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
#4: Protein Nuclease-like protein


Mass: 51918.312 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

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Non-polymers , 2 types, 31 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.35 Å3/Da / Density % sol: 8.91 %
Crystal growTemperature: 279 K / Method: evaporation / pH: 7 / Details: PEG10000 NaCl magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.975 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 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→59.79 Å / Num. all: 26454 / Num. obs: 26454 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 59.86 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.075 / Rrim(I) all: 0.182 / Net I/av σ(I): 2.4 / Net I/σ(I): 7.5 / Num. measured all: 218998
Reflection shellResolution: 2.4→2.57 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.376 / Mean I/σ(I) obs: 1.6 / Num. measured all: 26404 / Num. unique all: 5555 / Rpim(I) all: 1.495 / Net I/σ(I) obs: 0.4 / Rejects: 0 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.036 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1282 4.87 %Random selection
Rwork0.2388 25040 --
obs0.2396 26322 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.73 Å2 / Biso mean: 54.3946 Å2 / Biso min: 10.31 Å2
Refinement stepCycle: final / Resolution: 2.4→49.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6187 1196 2 29 7414
Biso mean--57.49 47.06 -
Num. residues----852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067666
X-RAY DIFFRACTIONf_angle_d0.87710628
X-RAY DIFFRACTIONf_chiral_restr0.0391175
X-RAY DIFFRACTIONf_plane_restr0.0041171
X-RAY DIFFRACTIONf_dihedral_angle_d19.6812933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.42431640.38192694285898
2.4961-2.60970.35191510.36662689284099
2.6097-2.74730.36761290.32452733286299
2.7473-2.91940.3511620.28972740290299
2.9194-3.14480.28741230.273227922915100
3.1448-3.46110.251440.230827622906100
3.4611-3.96180.21051300.209228312961100
3.9618-4.99070.18521530.191428262979100
4.9907-49.04610.26121260.229729733099100

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