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Yorodumi- PDB-1k97: Crystal Structure of E. coli Argininosuccinate Synthetase in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k97 | ||||||||||||
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Title | Crystal Structure of E. coli Argininosuccinate Synthetase in complex with Aspartate and Citrulline | ||||||||||||
Components | ARGININOSUCCINATE SYNTHASE | ||||||||||||
Keywords | LIGASE / N-TYPE ATP PYROPHOSPHATASE | ||||||||||||
Function / homology | Function and homology information argininosuccinate metabolic process / argininosuccinate synthase / argininosuccinate synthase activity / urea cycle / L-arginine biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Lemke, C.T. / Howell, P.L. | ||||||||||||
Citation | Journal: Structure / Year: 2001 Title: The 1.6 A crystal structure of E. coli argininosuccinate synthetase suggests a conformational change during catalysis. Authors: Lemke, C.T. / 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 | 1k97.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k97.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k97_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 1k97_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 1k97_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1k97_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k97 ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k97 | HTTPS FTP |
-Related structure data
Related structure data | 1k92C 1k91S 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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Details | The biological assembly is a tetramer from the monomer in the asymmetric unit by the operations: -X, -Y, Z and X, -Y, -Z and -X, Y, -Z |
-Components
#1: Protein | Mass: 50967.262 Da / Num. of mol.: 1 / Fragment: Residues 1 to 444 / Mutation: C-term tag SVEHHHHHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARGG / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / References: UniProt: P0A6E4, argininosuccinate synthase |
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#2: Chemical | ChemComp-ASP / |
#3: Chemical | ChemComp-CIR / |
#4: 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: 2.57 Å3/Da / Density % sol: 52.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Lemke, C., (1999) Acta Crystallogr., 55, 2028. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 35900 / Num. obs: 35667 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.7 Å2 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 97.6 % / Rmerge(I) obs: 0.265 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K91 Resolution: 2→20.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 810002.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1485 Å2 / ksol: 0.352627 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / 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: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.1757 / Rfactor Rfree: 0.2143 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.259 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.207 |