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Yorodumi- PDB-2yzl: Crystal structure of phosphoribosylaminoimidazole-succinocarboxam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yzl | ||||||
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Title | Crystal structure of phosphoribosylaminoimidazole-succinocarboxamide synthase with ADP from Methanocaldococcus jannaschii | ||||||
Components | Phosphoribosylaminoimidazole-succinocarboxamide synthase | ||||||
Keywords | LIGASE / 2-Layer Sandwich / Purine biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kanagawa, M. / Baba, S. / Fukui, K. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of phosphoribosylaminoimidazole-succinocarboxamide synthase with ADP from Methanocaldococcus jannaschii Authors: Kanagawa, M. / Baba, S. / Fukui, K. / Kuramitsu, S. / Yokoyama, S. / 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 | 2yzl.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzl.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzl ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzl | HTTPS FTP |
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-Related structure data
Related structure data | 1kutS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27803.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET-21a / Production host: Escherichia coli (E. coli) References: UniProt: Q58987, phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ADP / | #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: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.5M Ammmounium Sulfate, 0.1M Tris pH 8.5, 0.01M ADP, 0.01M Magnesium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 18, 2006 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 55697 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.312 / Num. unique all: 4687 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KUT Resolution: 2.2→41.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 69796.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.1441 Å2 / ksol: 0.364285 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→41.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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