+Open data
-Basic information
Entry | Database: PDB / ID: 4xm5 | ||||||
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Title | C. glabrata Slx1. | ||||||
Components | Structure-specific endonuclease subunit SLX1 | ||||||
Keywords | HYDROLASE / nuclease / DNA repair / GIY-YIG / homogolous recombination | ||||||
Function / homology | Function and homology information Slx1-Slx4 complex / 5'-flap endonuclease activity / DNA-templated DNA replication / DNA recombination / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å | ||||||
Authors | Gaur, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xm5.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xm5.ent.gz | 98.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/4xm5 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/4xm5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.4 M sodium citrate tribasic dihydrate and 0.1 M HEPES-NaOH (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.28 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.34→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.38 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→48.725 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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