+Open data
-Basic information
Entry | Database: PDB / ID: 1f3w | |||||||||
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Title | RECOMBINANT RABBIT MUSCLE PYRUVATE KINASE | |||||||||
Components | PYRUVATE KINASE | |||||||||
Keywords | TRANSFERASE / pyruvate kinase / recombinant / 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 / cellular response to insulin stimulus / protein tyrosine kinase activity / non-specific serine/threonine protein kinase ...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 / cellular response to insulin stimulus / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / mRNA binding / magnesium ion binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 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 | 1f3w.cif.gz | 759.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3w.ent.gz | 630.4 KB | Display | PDB format |
PDBx/mmJSON format | 1f3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f3w_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 1f3w_full_validation.pdf.gz | 593.3 KB | Display | |
Data in XML | 1f3w_validation.xml.gz | 99.1 KB | Display | |
Data in CIF | 1f3w_validation.cif.gz | 141.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3w ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | The biological assembly is a tetramer of homomonomers |
-Components
#1: Protein | Mass: 57982.820 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: 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 / |
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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: 2.37 Å3/Da / Density % sol: 48.01 % | ||||||||||||||||||||||||||||||||||||||||||
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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: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→52 Å / Num. all: 82732 / Num. obs: 82732 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.258 / Num. unique all: 9404 / % possible all: 93.2 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 82.9 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Resolution: 3→52 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3699007.04 / 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: Strict non-crystallographic symmetry followed by eight-fold density averaging
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.96 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→52 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.013 / 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: 52 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.247 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.362 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.366 |