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Yorodumi- PDB-1a3w: PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3w | ||||||
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Title | PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+ | ||||||
Components | PYRUVATE KINASE | ||||||
Keywords | TRANSFERASE / PYRUVATE KINASE / ALLOSTERIC REGULATION / TRANFERASE | ||||||
Function / homology | Function and homology information Pyruvate metabolism / Regulation of pyruvate metabolism / Glycolysis / pyruvate kinase / pyruvate kinase activity / pyruvate metabolic process / potassium ion binding / Neutrophil degranulation / glycolytic process / kinase activity ...Pyruvate metabolism / Regulation of pyruvate metabolism / Glycolysis / pyruvate kinase / pyruvate kinase activity / pyruvate metabolic process / potassium ion binding / Neutrophil degranulation / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Jurica, M.S. / Mesecar, A. / Heath, P.J. / Shi, W. / Nowak, T. / Stoddard, B.L. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate. Authors: Jurica, M.S. / Mesecar, A. / Heath, P.J. / Shi, W. / Nowak, T. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3w.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3w.ent.gz | 145.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3w_validation.pdf.gz | 516.2 KB | Display | wwPDB validaton report |
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Full document | 1a3w_full_validation.pdf.gz | 581.4 KB | Display | |
Data in XML | 1a3w_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 1a3w_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3w ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3w | HTTPS FTP |
-Related structure data
Related structure data | 1a3xC 1pknS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 54612.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00549, pyruvate kinase #2: Chemical | #3: Sugar | #4: Chemical | #5: Chemical | |
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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: 2.64 Å3/Da / Density % sol: 53.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 8, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→100 Å / Num. obs: 19294 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.065 |
Reflection | *PLUS Num. measured all: 66108 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PKN Resolution: 3→100 Å / Rfactor Rfree error: 0.0079 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→100 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 3→3.14 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.298 |