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Yorodumi- PDB-1ynf: Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ynf | ||||||
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Title | Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli | ||||||
Components | Succinylarginine dihydrolase | ||||||
Keywords | HYDROLASE / Succinylarginine / Dihydrolase | ||||||
Function / homology | Function and homology information N-succinylarginine dihydrolase / N-succinylarginine dihydrolase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate / arginine catabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.9 Å | ||||||
Authors | Tocilj, A. / Schrag, J.D. / Li, Y. / Schneider, B.L. / Reitzer, L. / Matte, A. / Cygler, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. Authors: Tocilj, A. / Schrag, J.D. / Li, Y. / Schneider, B.L. / Reitzer, L. / Matte, A. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ynf.cif.gz | 521.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ynf.ent.gz | 442.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ynf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1ynf ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1ynf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 50977.617 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76216, Hydrolases #2: Chemical | ChemComp-K / #3: 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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: PEG 10000, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Details: Osmic mirrors |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→27.32 Å / Num. all: 136811 / Observed criterion σ(F): 0 / Biso Wilson estimate: 16.6 Å2 / Limit h max: 24 / Limit h min: -24 / Limit k max: 48 / Limit k min: -24 / Limit l max: 63 / Limit l min: 0 / Observed criterion F max: 2459405.3 / Observed criterion F min: 48.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→27.32 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 44.6528 Å2 / ksol: 0.356305 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.42 Å2 / Biso mean: 26.1 Å2 / Biso min: 3.43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→27.32 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: 8
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Xplor file |
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