+Open data
-Basic information
Entry | Database: PDB / ID: 5lw0 | ||||||||||||||||||
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Title | Oryza sativa APL macrodomain in complex with ADP-ribose | ||||||||||||||||||
Components | Basic helix-loop-helix, putative, expressedBasic helix–loop–helix | ||||||||||||||||||
Keywords | ADP-RIBOSE-BINDING PROTEIN / ADP-ribosyltransferase / Interstrand crosslink repair | ||||||||||||||||||
Function / homology | Function and homology information purine ribonucleotide metabolic process / adenylylsulfatase activity / DNA 5'-adenosine monophosphate hydrolase activity / sulfur compound metabolic process / DNA repair / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||||||||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||||||||
Authors | Ariza, A. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: J.Cell.Sci. / Year: 2016 Title: The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. Authors: Gunn, A.R. / Banos-Pinero, B. / Paschke, P. / Sanchez-Pulido, L. / Ariza, A. / Day, J. / Emrich, M. / Leys, D. / Ponting, C.P. / Ahel, I. / Lakin, N.D. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lw0.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lw0.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lw0 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lw0 | HTTPS FTP |
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-Related structure data
Related structure data | 5lw6SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25386.852 Da / Num. of mol.: 2 / Fragment: UNP residues 78-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: LOC_Os03g18210 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q10MW4, UniProt: B8ALM5*PLUS #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 25% PEG 1500 + 0.1 M SPG buffer (succinic acid, sodium phosphate monobasic monohydrate and glycine) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2015 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→56.31 Å / Num. obs: 47191 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.875 / % possible all: 77.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LW6 Resolution: 1.65→56.31 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.788 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.533 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→56.31 Å
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Refine LS restraints |
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