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Yorodumi- PDB-3sij: The X-ray crystal structure of poly(ADP-ribose) glycohydrolase E1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sij | ||||||
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Title | The X-ray crystal structure of poly(ADP-ribose) glycohydrolase E115A mutant from Thermomonospora curvata | ||||||
Components | poly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Conserved hypothetical protein CHP02452 / Microbial-type PARG, catalytic domain / Microbial-type PARG, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta / Microbial-type PARG catalytic domain-containing protein Function and homology information | ||||||
Biological species | Thermomonospora curvata (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Dunstan, M.S. / Leys, D. | ||||||
Citation | Journal: Nature / Year: 2011 Title: The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Authors: Slade, D. / Dunstan, M.S. / Barkauskaite, E. / Weston, R. / Lafite, P. / Dixon, N. / Ahel, M. / Leys, D. / Ahel, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sij.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sij.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 3sij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sij_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 3sij_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 3sij_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 3sij_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/3sij ftp://data.pdbj.org/pub/pdb/validation_reports/si/3sij | HTTPS FTP |
-Related structure data
Related structure data | 3sigSC 3sihC 3siiC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29705.648 Da / Num. of mol.: 1 / Mutation: E115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_1721 / Production host: Escherichia coli (E. coli) References: UniProt: D1AC29, poly(ADP-ribose) glycohydrolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.43 % |
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Crystal grow | Method: sitting drop, vapor diffusion / pH: 9 Details: 10% PEG6000, 0.1 M Bicine, pH 9.0, SITTING DROP, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.251 Å / Num. all: 18831 / Num. obs: 18831 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SIG Resolution: 1.9→45.251 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8645 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.237 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.96 Å2 / Biso mean: 33.3747 Å2 / Biso min: 10.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.251 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 4.8747 Å / Origin y: -13.863 Å / Origin z: -13.2311 Å
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Refinement TLS group |
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