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- PDB-6s16: T. thermophilus RuvC in complex with Holliday junction substrate -

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Basic information

Entry
Database: PDB / ID: 6s16
TitleT. thermophilus RuvC in complex with Holliday junction substrate
Components
  • Crossover junction endodeoxyribonuclease RuvC
  • DNA (33-MER)
  • DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3')
KeywordsHYDROLASE / RuvC resolvase Holliday junction
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Crossover junction endodeoxyribonuclease RuvC / Crossover junction endodeoxyribonuclease RuvC / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Crossover junction endodeoxyribonuclease RuvC
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.409 Å
AuthorsGorecka, K.M. / Krepl, M. / Szlachcic, A. / Poznanski, J. / Sponer, J. / Nowotny, M.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000477 Czech Republic
Wellcome Trust098022
CitationJournal: Nat Commun / Year: 2019
Title: RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution.
Authors: Gorecka, K.M. / Krepl, M. / Szlachcic, A. / Poznanski, J. / Sponer, J. / Nowotny, M.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Crossover junction endodeoxyribonuclease RuvC
B: Crossover junction endodeoxyribonuclease RuvC
C: DNA (33-MER)
D: DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3')
F: DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6167
Polymers66,5585
Non-polymers582
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-76 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.066, 108.066, 133.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Crossover junction endodeoxyribonuclease RuvC / Holliday junction nuclease RuvC / Holliday junction resolvase RuvC


Mass: 18074.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: ruvC, TTHA1090 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SJC4, crossover junction endodeoxyribonuclease

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DNA chain , 2 types, 3 molecules CDF

#2: DNA chain DNA (33-MER)


Mass: 10136.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*TP*CP*TP*GP*CP*CP*GP*AP*TP*TP*C)-3')


Mass: 10136.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 3.4→38.3 Å / Num. obs: 12660 / % possible obs: 99.5 % / Redundancy: 5.6 % / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 16.8
Reflection shellResolution: 3.4→3.5 Å / Num. unique obs: 2003 / CC1/2: 0.717 / Rrim(I) all: 0.11

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD0

4ld0


Resolution: 3.409→38.296 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.2309 633 5 %
Rwork0.1812 --
obs0.1836 12660 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.409→38.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 1149 2 3 3479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013660
X-RAY DIFFRACTIONf_angle_d1.1655216
X-RAY DIFFRACTIONf_dihedral_angle_d19.6511955
X-RAY DIFFRACTIONf_chiral_restr0.057606
X-RAY DIFFRACTIONf_plane_restr0.007474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4091-3.67210.37351230.27562351X-RAY DIFFRACTION99
3.6721-4.04130.29941260.21032381X-RAY DIFFRACTION100
4.0413-4.62520.19711250.1522384X-RAY DIFFRACTION100
4.6252-5.8240.22951270.19112414X-RAY DIFFRACTION100
5.824-100.2061320.16582497X-RAY DIFFRACTION99

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