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Yorodumi- PDB-5a35: Crystal structure of Glycine Cleavage Protein H-Like (GcvH-L) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a35 | ||||||
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Title | Crystal structure of Glycine Cleavage Protein H-Like (GcvH-L) from Streptococcus pyogenes | ||||||
Components | GLYCINE CLEAVAGE SYSTEM H PROTEIN | ||||||
Keywords | TRANSPORT PROTEIN / LIPOYLATION / ADP-RIBOSYLATION | ||||||
Function / homology | Function and homology information glycine cleavage complex / glycine decarboxylation via glycine cleavage system Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 5a35.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a35.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 5a35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a35 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a35 | HTTPS FTP |
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-Related structure data
Related structure data | 5a3aC 5a3bC 5a3cC 1onlS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13263.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: MANFREDO / Variant: SEROTYPE M5 / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q1JGN4 | ||
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#2: Chemical | ChemComp-1PE / | ||
#3: Water | ChemComp-HOH / | ||
Nonpolymer details | PENTAETHYLSequence details | C-TERMINAL RESIDUES (GSGHHHHHHH | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.95 Å3/Da / Density % sol: 75.12 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 2.0 M NAH2PO4/K2HPO4 PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2014 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SINGLE BOUNCE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→55.53 Å / Num. obs: 28124 / % possible obs: 99.3 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ONL Resolution: 1.5→55.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.929 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES 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: 23.514 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→55.53 Å
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Refine LS restraints |
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