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Yorodumi- PDB-5a3c: Crystal structure of the ADP-ribosylating sirtuin (SirTM) from St... -
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-Basic information
Entry | Database: PDB / ID: 5a3c | ||||||
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Title | Crystal structure of the ADP-ribosylating sirtuin (SirTM) from Streptococcus pyogenes in complex with NAD | ||||||
Components | SIR2 FAMILY PROTEIN | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLTRANSFERASE / METALLOPROTEIN / NAD-DEPENDENT / LIPOYLATION / REGULATORY ENZYME / ROSSMANN FOLD / ZINC BINDING / ROS DEFENSE | ||||||
Function / homology | Sirtuin, catalytic core small domain superfamily / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / nucleotide binding / metal ion binding / GLYCINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SIR2 family protein Function and homology information | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å | ||||||
Authors | Rack, J.G.M. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. ...Rack, J.G.M. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. / Peleg, A.Y. / Leys, D. / Traven, A. / Ahel, I. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Identification of a Class of Protein Adp-Ribosylating Sirtuins in Microbial Pathogens. Authors: Rack, J.G. / Morra, R. / Barkauskaite, E. / Kraehenbuehl, R. / Ariza, A. / Qu, Y. / Ortmayer, M. / Leidecker, O. / Cameron, D.R. / Matic, I. / Peleg, A.Y. / Leys, D. / Traven, A. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a3c.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a3c.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3c ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3c | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35156.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: MANFREDO / Variant: SEROTYPE M5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q1JGN6, NAD+ ADP-ribosyltransferase |
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-Non-polymers , 5 types, 164 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-NAD / | #5: Chemical | #6: 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: 2.14 Å3/Da / Density % sol: 43.44 % Description: SAD DATA NOT DEPOSITED. SAD STRUCTURE WAS USED TO SUBSEQUENTLY SOLVE NATIVE STRUCTURES VIA MOLECULAR REPLACEMENT. |
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Crystal grow | pH: 8 Details: CRYSTALLIZATION CONDITIONS: 0.1 M AMINO ACIDS, 0.1 M BUFFER SYSTEM 1 (PH 6.5), 30.00% (V/V) EDO_P8K (THESE ARE COMPONENTS OF THE MORPHEUS SCREEN FROM MOLECULAR DIMENSIONS) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→40.82 Å / Num. obs: 17229 / % possible obs: 97.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / % possible all: 95.2 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.03→40.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.456 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS AND U VALUES WERE REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.811 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→40.82 Å
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