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- PDB-5yww: Archael RuvB-like Holiday junction helicase -

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Basic information

Entry
Database: PDB / ID: 5yww
TitleArchael RuvB-like Holiday junction helicase
ComponentsNucleotide binding protein PINc
KeywordsHYDROLASE / ATPase / Helicase
Function / homology
Function and homology information


four-way junction helicase activity / DNA recombination / DNA helicase / hydrolase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function
: / 5'-nuclease / Type II/IV secretion system protein / Type II/IV secretion system protein / Large family of predicted nucleotide-binding domains / PIN domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Holliday junction branch migration ATPase PINA
Similarity search - Component
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsZhai, B. / Yuan, Z. / Han, X. / DuPrez, K. / Shen, Y. / Fan, L.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction.
Authors: Zhai, B. / DuPrez, K. / Han, X. / Yuan, Z. / Ahmad, S. / Xu, C. / Gu, L. / Ni, J. / Fan, L. / Shen, Y.
History
DepositionNov 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Nucleotide binding protein PINc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2452
Polymers57,1531
Non-polymers921
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.116, 74.766, 107.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Nucleotide binding protein PINc


Mass: 57153.012 Da / Num. of mol.: 1 / Mutation: R147K, I199S, R206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Strain: REY15A / Gene: SiRe_1432 / Production host: Escherichia coli (E. coli) / References: UniProt: F0NID4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 287 K / Method: evaporation
Details: 0.1M Bis-tris pH 6.5, 20% PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24438 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rpim(I) all: 0.046 / Net I/σ(I): 32.38
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.44 / Rpim(I) all: 0.414 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4H

5f4h


Resolution: 2.33→19.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.336 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23642 1899 8.3 %RANDOM
Rwork0.20719 ---
obs0.20966 21020 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.265 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.33→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 6 79 3765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193737
X-RAY DIFFRACTIONr_bond_other_d0.0060.023583
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9815062
X-RAY DIFFRACTIONr_angle_other_deg1.02238269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38825.105143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024111
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02686
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5715.5931938
X-RAY DIFFRACTIONr_mcbond_other3.575.591937
X-RAY DIFFRACTIONr_mcangle_it5.4858.3752419
X-RAY DIFFRACTIONr_mcangle_other5.4848.3782420
X-RAY DIFFRACTIONr_scbond_it3.7395.9121799
X-RAY DIFFRACTIONr_scbond_other3.7225.9121799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9398.692644
X-RAY DIFFRACTIONr_long_range_B_refined8.29665.2973926
X-RAY DIFFRACTIONr_long_range_B_other8.29665.2983927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.329→2.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 130 -
Rwork0.29 1309 -
obs--81.21 %

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