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Yorodumi- PDB-1k62: Crystal Structure of the Human Argininosuccinate Lyase Q286R Mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k62 | ||||||
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Title | Crystal Structure of the Human Argininosuccinate Lyase Q286R Mutant | ||||||
Components | Argininosuccinate Lyase | ||||||
Keywords | LYASE / intragenic complementation / arginiosuccinate lyase / delta crystallin / enzyme mechanism | ||||||
Function / homology | Function and homology information ammonia assimilation cycle / argininosuccinate lyase / argininosuccinate lyase activity / arginine metabolic process / Urea cycle / arginine biosynthetic process via ornithine / urea cycle / arginine biosynthetic process / post-embryonic development / locomotory behavior ...ammonia assimilation cycle / argininosuccinate lyase / argininosuccinate lyase activity / arginine metabolic process / Urea cycle / arginine biosynthetic process via ornithine / urea cycle / arginine biosynthetic process / post-embryonic development / locomotory behavior / positive regulation of nitric oxide biosynthetic process / extracellular exosome / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Sampaleanu, L.M. / Vallee, F. / Thompson, G.D. / Howell, P.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Three-dimensional structure of the argininosuccinate lyase frequently complementing allele Q286R. Authors: Sampaleanu, L.M. / Vallee, F. / Thompson, G.D. / Howell, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k62.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k62.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k62_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 1k62_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 1k62_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 1k62_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k62 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k62 | HTTPS FTP |
-Related structure data
Related structure data | 1auwS 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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Details | The biological assembly is a homotetramer generated from the dimer in the asymmetric unit by the operation: -x, y-x, 1/3-z |
-Components
#1: Protein | Mass: 51934.164 Da / Num. of mol.: 2 / Mutation: Q286R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04424, argininosuccinate lyase #2: 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: 2.76 Å3/Da / Density % sol: 55.45 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1 M phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.1 Details: Turner, M.A., (1997) Proc.Natl.Acad.Sci.USA, 94, 9063. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999 |
Radiation | Monochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→17 Å / Num. all: 79294 / Num. obs: 79294 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.1 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.65→2.74 Å / Rsym value: 0.46 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 17 Å / Num. obs: 33242 / Num. measured all: 79294 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUW Resolution: 2.65→16.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8156643.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2174 Å2 / ksol: 0.310664 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→16.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 17 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.258 |