+Open data
-Basic information
Entry | Database: PDB / ID: 1fw8 | ||||||
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Title | CIRCULARLY PERMUTED PHOSPHOGLYCERATE KINASE FROM YEAST: PGK P72 | ||||||
Components | Phosphoglycerate kinase | ||||||
Keywords | TRANSFERASE / phosphotransferase / kinase / phosphoglycerate kinase / glycolysis / mutant / permutation / permuted sequence / PGK / protein folding / two-domain protein | ||||||
Function / homology | Function and homology information Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / ADP binding / gluconeogenesis / glycolytic process / phosphorylation / mitochondrion / ATP binding ...Gluconeogenesis / Glycolysis / phosphoglycerate kinase / phosphoglycerate kinase activity / ADP binding / gluconeogenesis / glycolytic process / phosphorylation / mitochondrion / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Tougard, P. / Bizebard, T. / Ritco-Vonsovici, M. / Minard, P. / Desmadril, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of a circularly permuted phosphoglycerate kinase. Authors: Tougard, P. / Bizebard, T. / Ritco-Vonsovici, M. / Minard, P. / Desmadril, M. #1: Journal: Biochemistry / Year: 1995 Title: Is the continuity of the domains required for the correct folding of a two-domain protein? Authors: Ritco-Vonsovici, M. / Minard, P. / Desmadril, M. / Yon, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fw8.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fw8.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/1fw8 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/1fw8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44654.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: PGK1, YCR012W, YCR12W / Plasmid: PYE / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00560, phosphoglycerate kinase | ||
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#2: Chemical | ChemComp-GOL / #3: 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: 2.23 Å3/Da / Density % sol: 44.82 % | |||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: ammonium sulfate, sodium pyrophosphate, dioxan, glycerol for cryogenic conditions, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→14.99 Å / Num. all: 18305 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 2.3→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.273 / Num. unique all: 1787 / % possible all: 99.4 |
Reflection | *PLUS Num. obs: 18306 / Num. measured all: 64243 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Resolution: 2.3→7 Å
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Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS σ(I): 16817 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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