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- PDB-7bnx: Archeal holliday junction resolvase from Thermus thermophilus pha... -

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Basic information

Entry
Database: PDB / ID: 7bnx
TitleArcheal holliday junction resolvase from Thermus thermophilus phage 15-6
ComponentsHolliday junction resolvase
KeywordsRECOMBINATION / archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus
Function / homologyTrna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesThermus thermophilus phage 15-6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsHakansson, M. / Ahlqvist, J. / Linares Pasten, J.A. / Jasilionis, A. / Nordberg Karlsson, E. / Al-Karadaghi, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)685778European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6.
Authors: Ahlqvist, J. / Linares-Pasten, J.A. / Hakansson, M. / Jasilionis, A. / Kwiatkowska-Semrau, K. / Friðjonsson, O.H. / Kaczorowska, A.K. / Dabrowski, S. / Aevarsson, A. / Hreggvið ...Authors: Ahlqvist, J. / Linares-Pasten, J.A. / Hakansson, M. / Jasilionis, A. / Kwiatkowska-Semrau, K. / Friðjonsson, O.H. / Kaczorowska, A.K. / Dabrowski, S. / Aevarsson, A. / Hreggviðsson, G.O. / Al-Karadaghi, S. / Kaczorowski, T. / Nordberg Karlsson, E.
History
DepositionJan 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Holliday junction resolvase
B: Holliday junction resolvase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12210
Polymers37,3532
Non-polymers7698
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.71, 104.17, 84.86
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

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Components

#1: Protein Holliday junction resolvase


Mass: 18676.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus phage 15-6 (virus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.8 M Ammoniumsulphate and 0.1 M sodiumacetate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7701 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7701 Å / Relative weight: 1
ReflectionResolution: 2.55→29 Å / Num. obs: 14269 / % possible obs: 99.8 % / Redundancy: 50.9 % / CC1/2: 1 / Net I/σ(I): 47.2
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.698 / Num. unique obs: 1682 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BGS

7bgs


Resolution: 2.551→28.95 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.334 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 703 -RANDOM
Rwork0.2287 ---
obs0.23 14253 99.8 %-
Displacement parametersBiso mean: 89.95 Å2
Baniso -1Baniso -2Baniso -3
1--3.5696 Å20 Å20 Å2
2--17.4659 Å20 Å2
3----13.8963 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.551→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 40 32 2030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092041HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d656SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it2041HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion255SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1509SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion15.96
LS refinement shellResolution: 2.551→2.58 Å
RfactorNum. reflection% reflection
Rfree0.3453 24 -
Rwork0.2986 --
obs--95.6 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.10825.4946-1.302610.5832-1.49715.21720.48390.78220.26830.7822-0.579-0.24860.2683-0.24860.0951-0.0031-0.1999-0.02830.08060.19460.10737.03339.439173.8956
26.83594.91491.440616.63095.82089.75730.48790.7989-0.43950.79890.11280.525-0.43950.525-0.6006-0.045-0.15530.0328-0.0019-0.1595-0.00989.3225-13.325475.0462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|149 }A5 - 149
2X-RAY DIFFRACTION2{ B|5 - B|150 }B5 - 150

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