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- PDB-4xm5: C. glabrata Slx1. -

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Basic information

Entry
Database: PDB / ID: 4xm5
TitleC. glabrata Slx1.
ComponentsStructure-specific endonuclease subunit SLX1
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 / Hydrolases; Acting on ester bonds / zinc ion binding
Similarity search - Function
: / Structure-specific endonuclease subunit SLX1, C-terminal / Structure-specific endonuclease subunit Slx1 / : / 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 SLX1
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 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 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Structure-specific endonuclease subunit SLX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6484
Polymers36,4821
Non-polymers1663
Water1,856103
1
A: Structure-specific endonuclease subunit SLX1
hetero molecules

A: Structure-specific endonuclease subunit SLX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2968
Polymers72,9632
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4060 Å2
ΔGint-43 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.486, 57.486, 183.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Structure-specific endonuclease subunit SLX1


Mass: 36481.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: SLX1, CAGL0K06941g / Production host: Escherichia coli (E. coli)
References: UniProt: Q6FML9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.4 M sodium citrate tribasic dihydrate and 0.1 M HEPES-NaOH (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.28 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 24808 / % possible obs: 99.95 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.31
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.38 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→48.725 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2495 10.06 %
Rwork0.1912 --
obs0.1972 24808 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→48.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 3 103 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092148
X-RAY DIFFRACTIONf_angle_d1.1052912
X-RAY DIFFRACTIONf_dihedral_angle_d13.971754
X-RAY DIFFRACTIONf_chiral_restr0.042328
X-RAY DIFFRACTIONf_plane_restr0.006366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.38510.3511370.27061281X-RAY DIFFRACTION99
2.3851-2.43380.35651270.27611219X-RAY DIFFRACTION100
2.4338-2.48670.33041410.24691235X-RAY DIFFRACTION100
2.4867-2.54460.35411410.23271227X-RAY DIFFRACTION100
2.5446-2.60820.29221440.23491275X-RAY DIFFRACTION100
2.6082-2.67870.27861310.23571197X-RAY DIFFRACTION100
2.6787-2.75760.27351380.21991252X-RAY DIFFRACTION100
2.7576-2.84660.25291400.21511245X-RAY DIFFRACTION100
2.8466-2.94830.29341380.20341233X-RAY DIFFRACTION100
2.9483-3.06630.29991400.2061233X-RAY DIFFRACTION100
3.0663-3.20580.29021410.20091241X-RAY DIFFRACTION100
3.2058-3.37480.22341400.16681254X-RAY DIFFRACTION100
3.3748-3.58620.22611440.1741233X-RAY DIFFRACTION100
3.5862-3.8630.23461410.15361240X-RAY DIFFRACTION100
3.863-4.25150.19441340.15751222X-RAY DIFFRACTION100
4.2515-4.86620.20711350.14961243X-RAY DIFFRACTION100
4.8662-6.12910.2531400.19291243X-RAY DIFFRACTION100
6.1291-48.73520.24321430.21321240X-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)
14.01931.1375-1.89973.984-1.46054.1337-0.016-0.324-0.28560.1492-0.017-0.08460.33650.31860.01520.3050.05070.03680.31660.01440.245724.681616.418460.425
22.87112.6577-0.7476.4449-1.25091.80890.6998-0.48520.75310.8419-0.03390.4862-0.78790.6974-0.6470.5204-0.09720.23410.5316-0.14730.428623.862733.079567.7394
33.45292.2577-0.63551.83040.41984.52320.6727-1.31160.81540.6058-0.1765-0.1073-0.83531.407-0.33780.6405-0.30080.16210.8098-0.17210.493242.672939.043754.5971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 215 )
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 303 )

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