+Open data
-Basic information
Entry | Database: PDB / ID: 1f3x | |||||||||
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Title | S402P MUTANT OF RABBIT MUSCLE PYRUVATE KINASE | |||||||||
Components | PYRUVATE KINASE | |||||||||
Keywords | TRANSFERASE / pyruvate kinase / S402P / muscle isozyme | |||||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation ...pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / non-specific protein-tyrosine kinase / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / phosphorylation / mRNA binding / magnesium ion binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | |||||||||
Authors | Wooll, J.O. / Friesen, R.H.E. / White, M.A. / Watowich, S.J. / Fox, R.O. / Lee, J.C. / Czerwinski, E.W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structural and functional linkages between subunit interfaces in mammalian pyruvate kinase. Authors: Wooll, J.O. / Friesen, R.H. / White, M.A. / Watowich, S.J. / Fox, R.O. / Lee, J.C. / Czerwinski, E.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f3x.cif.gz | 770 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3x.ent.gz | 636.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3x ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3x | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9999, 0.00019, 0.01408), Vector: Details | The biological assembly is a tetramer of homomonomers | |
-Components
#1: Protein | Mass: 57992.852 Da / Num. of mol.: 8 / Mutation: S402P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / Plasmid: PRMPK / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P11974, pyruvate kinase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-PYR / #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: 2.55 Å3/Da / Density % sol: 51.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, manganese chloride, potassium chloride, sodium pyruvate, succinate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2000H / Detector: IMAGE PLATE / Date: Dec 30, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→36 Å / Num. all: 92167 / Num. obs: 92167 / % possible obs: 81.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.256 / Num. unique all: 15897 / % possible all: 79.2 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 79.2 % / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Resolution: 2.8→36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3457707.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Restrained non-crystallographic symmetry followed by two-fold density averaging. Overall R after averaging = 0.113, Correlation Coefficient = 0.963.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.53 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→36 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 36 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.273 / Rfactor Rfree: 0.239 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.368 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.343 |