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Yorodumi- PDB-1x8e: Crystal structure of Pyrococcus furiosus phosphoglucose isomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x8e | ||||||
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Title | Crystal structure of Pyrococcus furiosus phosphoglucose isomerase free enzyme | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / CUPIN SUPERFAMILY / PYROCOCCUS FURIOSUS / HYPERTHERMOPHILE / PHOSPHOGLUCOSE ISOMERASE / EXTREMEOPHILE | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Berrisford, J.M. / Akerboom, J. / Brouns, S. / Sedelnikova, S.E. / Turnbull, A.P. / van der Oost, J. / Salmon, L. / Hardre, R. / Murray, I.A. / Blackburn, G.M. ...Berrisford, J.M. / Akerboom, J. / Brouns, S. / Sedelnikova, S.E. / Turnbull, A.P. / van der Oost, J. / Salmon, L. / Hardre, R. / Murray, I.A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis. Authors: Berrisford, J.M. / Akerboom, J. / Brouns, S. / Sedelnikova, S.E. / Turnbull, A.P. / van der Oost, J. / Salmon, L. / Hardre, R. / Murray, I.A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x8e.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x8e.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 1x8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/1x8e ftp://data.pdbj.org/pub/pdb/validation_reports/x8/1x8e | HTTPS FTP |
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-Related structure data
Related structure data | 1x7nC 1x82SC 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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Details | Subunits A and B generate the biological dimer |
-Components
#1: Protein | Mass: 21636.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pgiA / Plasmid: PET24-d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83194, glucose-6-phosphate isomerase |
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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: 2.1 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M tri-sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 2003 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→53.45 Å / Num. all: 10198 / Num. obs: 10096 / % possible obs: 99 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1359 / % possible all: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X82 Resolution: 2.8→53.45 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.85 / SU B: 19.835 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.614 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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