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Yorodumi- PDB-1j1z: Crystal Structure of Thermus thermophilus HB8 Argininosuccinate S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j1z | |||||||||
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Title | Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with substrate | |||||||||
Components | Argininosuccinate Synthetase | |||||||||
Keywords | LIGASE / ATP-binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Goto, M. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structures of argininosuccinate synthetase in enzyme-ATP-substrates and enzyme-AMP-product forms Authors: Goto, M. / Omi, R. / Miyahara, I. / Sugahara, M. / Hirotsu, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j1z.cif.gz | 326 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j1z.ent.gz | 264.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j1z_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1j1z_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 1j1z_validation.xml.gz | 67.7 KB | Display | |
Data in CIF | 1j1z_validation.cif.gz | 91.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j1z ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j1z | HTTPS FTP |
-Related structure data
Related structure data | 1j20C 1j21C 1kh3C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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-ATP / #3: Chemical | ChemComp-CIR / #4: Chemical | ChemComp-ASP / #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: 4.38 Å3/Da / Density % sol: 71.68 % | ||||||||||||||||||||||||||||||
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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 Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 178320 / Num. obs: 178320 / % possible obs: 98.2 % |
Reflection shell | Resolution: 2.1→2.17 Å / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 561786 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / σ(F): 2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.2571 / Rfactor Rwork: 0.2327 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.43 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3392 / Rfactor Rwork: 0.3034 |