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Yorodumi- PDB-1kh1: Crystal Structure of Thermus thermophilus HB8 Argininosuccinate S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kh1 | ||||||
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Title | Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase | ||||||
Components | Argininosuccinate Synthetase | ||||||
Keywords | LIGASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information argininosuccinate metabolic process / argininosuccinate synthase / argininosuccinate synthase activity / urea cycle / arginine biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Goto, M. / Nakajima, Y. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action. Authors: Goto, M. / Nakajima, Y. / Hirotsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kh1.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kh1.ent.gz | 253.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kh1_validation.pdf.gz | 476.2 KB | Display | wwPDB validaton report |
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Full document | 1kh1_full_validation.pdf.gz | 515.8 KB | Display | |
Data in XML | 1kh1_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 1kh1_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/1kh1 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/1kh1 | HTTPS FTP |
-Related 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: 44875.992 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P59846, argininosuccinate synthase #2: Chemical | ChemComp-SO4 / #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: 4.52 Å3/Da / Density % sol: 72.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: tris, ammonium sulfate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.8 Å / Num. all: 124435 / Num. obs: 124435 / % possible obs: 89.2 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 2.3→2.37 Å / % possible all: 78.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 281918 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 78.3 % / Rmerge(I) obs: 0.127 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→10 Å / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 48.8 Å / Rfactor obs: 0.1994 / Rfactor Rfree: 0.2291 / Rfactor Rwork: 0.1994 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.2907 / Rfactor Rwork: 0.2525 / Rfactor obs: 0.2525 |