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- PDB-4zdt: Crystal structure of the RING finger domain of Slx1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4zdt
TitleCrystal structure of the RING finger domain of Slx1 in complex with the C-terminal domain of Slx4
Components(Structure-specific endonuclease subunit ...) x 2
KeywordsHYDROLASE / RING finger / Endonuclease
Function / homology
Function and homology information


meiotic DNA double-strand break processing / rDNA protrusion / Slx1-Slx4 complex / double-stranded DNA endonuclease activity / maintenance of rDNA / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / 5'-flap endonuclease activity / mitotic DNA replication / double-strand break repair via break-induced replication ...meiotic DNA double-strand break processing / rDNA protrusion / Slx1-Slx4 complex / double-stranded DNA endonuclease activity / maintenance of rDNA / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / 5'-flap endonuclease activity / mitotic DNA replication / double-strand break repair via break-induced replication / replication fork processing / interstrand cross-link repair / double-strand break repair via homologous recombination / Hydrolases; Acting on ester bonds / metal ion binding / nucleus
Similarity search - Function
Structure-specific endonuclease subunit Slx1 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type ...Structure-specific endonuclease subunit Slx1 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Structure-specific endonuclease subunit slx4 / Structure-specific endonuclease subunit slx1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLian, F.M. / Xie, S. / Qian, C.M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong Research Grants Council Hong Kong
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure and SUMO binding of Slx1-Slx4 complex
Authors: Lian, F.M. / Xie, S. / Qian, C.M.
History
DepositionApr 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structure-specific endonuclease subunit slx1
B: Structure-specific endonuclease subunit slx4
C: Structure-specific endonuclease subunit slx1
D: Structure-specific endonuclease subunit slx4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,18914
Polymers33,3714
Non-polymers81810
Water1,928107
1
A: Structure-specific endonuclease subunit slx1
B: Structure-specific endonuclease subunit slx4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0937
Polymers16,6852
Non-polymers4075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-12 kcal/mol
Surface area8520 Å2
MethodPISA
2
C: Structure-specific endonuclease subunit slx1
D: Structure-specific endonuclease subunit slx4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0967
Polymers16,6852
Non-polymers4115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-27 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.233, 85.233, 74.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Structure-specific endonuclease subunit ... , 2 types, 4 molecules ACBD

#1: Protein Structure-specific endonuclease subunit slx1


Mass: 8423.784 Da / Num. of mol.: 2 / Fragment: UNP residues 176-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: slx1, SPAP27G11.15 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q9P7M3, Hydrolases; Acting on ester bonds
#2: Protein Structure-specific endonuclease subunit slx4 / Synthetic lethal of unknown function protein 4


Mass: 8261.644 Da / Num. of mol.: 2 / Fragment: UNP residues 356-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: slx4, SPAC688.06c / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P6M0

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Non-polymers , 4 types, 117 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 1.34M ammonium sulfate, 0.1M Bis-Tris, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.28238 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28238 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 36121 / Num. obs: 36121 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 28.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
SCALEPACKdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.1 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23631 1729 4.8 %RANDOM
Rwork0.21511 ---
obs0.21617 34383 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.398 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.68 Å2
Refinement stepCycle: 1 / Resolution: 2→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 39 107 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222283
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9613072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8195273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9324.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88515432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021606
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8491.51378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59122242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0853905
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4624.5830
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 114 -
Rwork0.263 2472 -
obs--97.66 %

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