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- PDB-4xlg: C. glabrata Slx1 in complex with Slx4CCD. -

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Basic information

Entry
Database: PDB / ID: 4xlg
TitleC. glabrata Slx1 in complex with Slx4CCD.
Components
  • Structure-specific endonuclease subunit SLX1
  • Structure-specific endonuclease subunit SLX4
KeywordsHYDROLASE / nuclease / DNA repair / GIY-YIG / homogolous recombination
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 / DNA-templated DNA replication / DNA recombination / Hydrolases; Acting on ester bonds / DNA replication / DNA repair / zinc ion binding
Similarity search - Function
Structure-specific endonuclease subunit Slx4, ascomycetes / : / Structure-specific endonuclease subunit SLX1, C-terminal / Structure-specific endonuclease subunit Slx1 / : / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG endonuclease superfamily ...Structure-specific endonuclease subunit Slx4, ascomycetes / : / Structure-specific endonuclease subunit SLX1, C-terminal / Structure-specific endonuclease subunit Slx1 / : / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG endonuclease superfamily / GIY-YIG catalytic domain / GIY-YIG domain profile. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Structure-specific endonuclease subunit SLX4 / Structure-specific endonuclease subunit SLX1
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsGaur, V. / Wyatt, H.D.M. / Komorowska, W. / Szczepanowski, R.H. / de Sanctis, D. / Gorecka, K.M. / West, S.C. / Nowotny, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust98022 United Kingdom
CitationJournal: Cell Rep / Year: 2015
Title: Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease.
Authors: Gaur, V. / Wyatt, H.D. / Komorowska, W. / Szczepanowski, R.H. / de Sanctis, D. / Gorecka, K.M. / West, S.C. / Nowotny, M.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Structure-specific endonuclease subunit SLX4
A: Structure-specific endonuclease subunit SLX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9976
Polymers45,7952
Non-polymers2024
Water5,441302
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-35 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.790, 135.790, 56.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Structure-specific endonuclease subunit SLX4


Mass: 9313.671 Da / Num. of mol.: 1 / Fragment: unp residues 647-726
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Gene: SLX4, CAGL0M04389g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FJQ6
#2: Protein Structure-specific endonuclease subunit SLX1


Mass: 36481.504 Da / Num. of mol.: 1 / Mutation: E79Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Gene: SLX1, CAGL0K06941g / Production host: Escherichia coli (E. coli)
References: UniProt: Q6FML9, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Bis Tris (pH 6.5), 25% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.78→40 Å / Num. all: 57362 / Num. obs: 57362 / % possible obs: 99.98 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.3
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.25 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XM5

4xm5


Resolution: 1.78→40 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 2818 4.91 %
Rwork0.1578 --
obs0.1589 57362 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 4 302 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182765
X-RAY DIFFRACTIONf_angle_d1.4613754
X-RAY DIFFRACTIONf_dihedral_angle_d13.6571028
X-RAY DIFFRACTIONf_chiral_restr0.095427
X-RAY DIFFRACTIONf_plane_restr0.008472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.81070.24311380.23422714X-RAY DIFFRACTION100
1.8107-1.84370.2531700.22122664X-RAY DIFFRACTION100
1.8437-1.87910.29921120.21552737X-RAY DIFFRACTION100
1.8791-1.91750.22711240.20182712X-RAY DIFFRACTION100
1.9175-1.95920.23721590.18932711X-RAY DIFFRACTION100
1.9592-2.00470.21231350.17332693X-RAY DIFFRACTION100
2.0047-2.05490.19071540.16552729X-RAY DIFFRACTION100
2.0549-2.11040.21061220.15312722X-RAY DIFFRACTION100
2.1104-2.17250.19391490.14892683X-RAY DIFFRACTION100
2.1725-2.24270.17741360.14382739X-RAY DIFFRACTION100
2.2427-2.32280.15351320.13862733X-RAY DIFFRACTION100
2.3228-2.41580.17191570.14812704X-RAY DIFFRACTION100
2.4158-2.52570.19171310.1532732X-RAY DIFFRACTION100
2.5257-2.65890.16281640.15012700X-RAY DIFFRACTION100
2.6589-2.82550.20581540.14442719X-RAY DIFFRACTION100
2.8255-3.04360.20381350.15412734X-RAY DIFFRACTION100
3.0436-3.34980.17441640.15282729X-RAY DIFFRACTION100
3.3498-3.83420.15361200.14572762X-RAY DIFFRACTION100
3.8342-4.82980.15271520.13922759X-RAY DIFFRACTION100
4.8298-44.46160.19321100.18332868X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / 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)
11.53061.247-0.55153.3613-0.2450.31030.17380.04890.27030.15870.03050.2288-0.52730.22870.08030.5184-0.17060.02920.30240.00610.3438-48.010336.5673-1.814
21.58160.8310.662.26020.89491.8902-0.06610.11170.0663-0.22660.01970.0105-0.24950.12230.02320.2917-0.01340.00370.14090.01430.1963-60.622411.7475-9.8215
32.87651.54361.21292.50310.47032.2676-0.12870.3491-0.4052-0.29280.2585-0.5473-0.01690.495-0.12230.31110.03380.06250.293-0.06760.3311-52.46530.5191-15.96
42.62131.7591.93111.98011.80513.56870.4119-0.2595-0.26960.4673-0.1555-0.27830.5333-0.0658-0.12970.3380.0104-0.03680.13780.03420.2297-58.76370.99743.0393
52.68040.49550.67172.3993-0.31282.89580.1922-0.491-0.15060.4887-0.3115-0.3909-0.02750.7894-0.140.3993-0.1075-0.0740.48130.06390.3661-40.8218.324711.7187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 655 through 721 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 214 )
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 300 )

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