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Yorodumi- PDB-3o98: Glutathionylspermidine synthetase/amidase C59A complex with ADP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o98 | ||||||
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Title | Glutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp | ||||||
Components | Bifunctional glutathionylspermidine synthetase/amidase | ||||||
Keywords | Ligase / Hydrolase | ||||||
Function / homology | Function and homology information glutathionylspermidine amidase / glutathionylspermidine synthase / glutathionylspermidine amidase activity / glutathionylspermidine synthase activity / spermidine metabolic process / glutathione metabolic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pai, C.H. / Lin, C.H. / Wang, A.H.-J. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases Authors: Pai, C.-H. / Wu, H.-J. / Lin, C.-H. / Wang, A.H.-J. #1: Journal: Embo J. / Year: 2006 Title: Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase Authors: Pai, C.H. / Chiang, B.Y. / Ko, T.P. / Chou, C.C. / Chong, C.M. / Yen, F.J. / Chen, S. / Coward, J.K. / Wang, A.H.-J. / Lin, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o98.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o98.ent.gz | 204.5 KB | Display | PDB format |
PDBx/mmJSON format | 3o98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/3o98 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o98 | HTTPS FTP |
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-Related structure data
Related structure data | 3a2yC 2iobS 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: 70579.672 Da / Num. of mol.: 2 / Mutation: C59A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) References: UniProt: P0AES0, glutathionylspermidine synthase, glutathionylspermidine amidase #2: Chemical | ChemComp-TS5 / | #3: Chemical | #4: Chemical | ChemComp-MG / #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: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 12% PEG 3350, 0.5M MgCl2, 0.1M Tris pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 32519 / Num. obs: 31316 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2iob Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree: 0.3278 / Rfactor Rwork: 0.2808 |