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Yorodumi- PDB-6jrq: Crystal structure of adenylosuccinate synthetase, PurA, from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jrq | ||||||
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Title | Crystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus | ||||||
Components | Adenylosuccinate synthetaseAdenylosuccinate synthase | ||||||
Keywords | LIGASE / purine / IMP / complex / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus HB8 Authors: Ishii, H. / Taka, H. / Kawai, G. / Sampei, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jrq.cif.gz | 330.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jrq.ent.gz | 268.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/6jrq ftp://data.pdbj.org/pub/pdb/validation_reports/jr/6jrq | HTTPS FTP |
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-Related structure data
Related structure data | 1dj3S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44947.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5SLS1, adenylosuccinate synthase #2: Chemical | ChemComp-IMP / #3: Chemical | ChemComp-EDO / #4: 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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: PEG 8000, Ethylene Glycol, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007 |
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→34.47 Å / Num. obs: 101788 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 8.754 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.048 / Rrim(I) all: 0.082 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5002 / CC1/2: 0.97 / Rpim(I) all: 0.119 / Rrim(I) all: 0.206 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DJ3 Resolution: 2.1→34.47 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.9 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.368 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→34.47 Å
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Refine LS restraints |
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