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- PDB-7wme: Crystal Structure of the catalytic domain of At-HIGLE -

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Basic information

Entry
Database: PDB / ID: 7wme
TitleCrystal Structure of the catalytic domain of At-HIGLE
ComponentsStructure-specific endonuclease subunit SLX1 homolog
KeywordsPLANT PROTEIN / Resolvase Nuclease Structure-selective endonuclease
Function / homology
Function and homology information


Slx1-Slx4 complex / crossover junction DNA endonuclease activity / 5'-flap endonuclease activity / double-strand break repair via homologous recombination / Hydrolases; Acting on ester bonds
Similarity search - Function
Structure-specific endonuclease subunit Slx1 / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily
Similarity search - Domain/homology
Structure-specific endonuclease subunit SLX1 homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVerma, P. / Kumari, P. / Negi, S. / Yadav, G. / Gaur, V.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/RLF/Re-entry/27/2017 India
Department of Science & Technology (DST, India)CRG/2020/000335 India
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism.
Authors: Verma, P. / Kumari, P. / Negi, S. / Yadav, G. / Gaur, V.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structure-specific endonuclease subunit SLX1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8162
Polymers20,7761
Non-polymers401
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-2 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.518, 53.452, 69.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Structure-specific endonuclease subunit SLX1 homolog / HIGLE


Mass: 20775.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: Q682H4, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.82 Å3/Da / Density % sol: 32.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 4M Sodium Formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.7→32.29 Å / Num. obs: 17294 / % possible obs: 99.94 % / Redundancy: 12.6 % / Biso Wilson estimate: 16.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1223 / Net I/σ(I): 15.86
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.6415 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 1712 / CC1/2: 0.919 / CC star: 0.979 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MxCuBE3data collection
XDSVERSION Feb 5, 2021 BUILT=20210323data scaling
PHENIX1.16-3549-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XM5

4xm5


Resolution: 1.7→32.29 Å / SU ML: 0.1567 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.3269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 1730 10 %
Rwork0.1637 15562 -
obs0.1667 17292 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 1 131 1326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421266
X-RAY DIFFRACTIONf_angle_d1.30671731
X-RAY DIFFRACTIONf_chiral_restr0.0851189
X-RAY DIFFRACTIONf_plane_restr0.0089216
X-RAY DIFFRACTIONf_dihedral_angle_d3.10931000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.22931390.18691253X-RAY DIFFRACTION100
1.75-1.810.24731420.16751276X-RAY DIFFRACTION100
1.81-1.870.20751440.15481289X-RAY DIFFRACTION100
1.87-1.950.20691410.1451275X-RAY DIFFRACTION100
1.95-2.030.19591410.1471271X-RAY DIFFRACTION100
2.03-2.140.16461440.13751298X-RAY DIFFRACTION100
2.14-2.280.17811420.15131271X-RAY DIFFRACTION100
2.28-2.450.22561420.16331289X-RAY DIFFRACTION100
2.45-2.70.20221460.16461314X-RAY DIFFRACTION99.93
2.7-3.090.21841450.16931294X-RAY DIFFRACTION100
3.09-3.890.17341480.15731333X-RAY DIFFRACTION100
3.89-32.290.18171560.18541399X-RAY DIFFRACTION100

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