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

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Basic information

Entry
Database: PDB / ID: 7bgs
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 / SAD / MAD / Resolution: 2.5 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 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)38,68410
Polymers37,9162
Non-polymers7698
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Dimer of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.58, 103.71, 84.85
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-309-

HOH

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Components

#1: Protein Holliday junction resolvase


Mass: 18957.945 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.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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
Details: 1.8 M ammonium sulphate and 0.1 M sodium acetate pH 4.2
PH range: 4.2 - 4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→29.2 Å / Num. obs: 253474 / % possible obs: 99.9 % / Redundancy: 16.7 % / CC1/2: 0.999 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 17436 / CC1/2: 0.631

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.319 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.317 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 765 -RANDOM
Rwork0.236 ---
obs0.2372 15236 100 %-
Displacement parametersBiso mean: 93.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.9756 Å20 Å20 Å2
2--15.2373 Å20 Å2
3----13.2617 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 40 37 2063
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092069HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.942811HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d677SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it2069HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion255SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1476SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion16.08
LS refinement shellResolution: 2.5→2.52 Å
RfactorNum. reflection% reflection
Rfree0.3623 26 -
Rwork0.332 --
obs0.334 401 100 %
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)
112.35184.3654-1.1489.8181-1.29185.63260.28520.71040.36910.7104-0.4577-0.24220.3691-0.24220.1725-0.0913-0.15820.0125-0.13640.1331-0.033537.29489.230273.7437
27.34166.2310.410619.93825.550211.28750.66210.8766-0.33510.87660.06060.4621-0.33510.4621-0.7227-0.0492-0.15830.0405-0.1328-0.142-0.14019.5721-13.390675.1357
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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