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Yorodumi- PDB-1x82: CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FUR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x82 | |||||||||
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Title | CRYSTAL STRUCTURE OF PHOSPHOGLUCOSE ISOMERASE FROM PYROCOCCUS FURIOSUS WITH BOUND 5-phospho-D-arabinonate | |||||||||
Components | Glucose-6-phosphate isomerase | |||||||||
Keywords | METAL BINDING PROTEIN / CUPIN SUPERFAMILY / PYROCOCCUS FURIOSUS / HYPERTHERMOPHILE / PHOSPHOGLUCOSE ISOMERASE / EXTREMEOPHILE / 5-phospho-D-arabinonate | |||||||||
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 / SYNCHROTRON / SAD / Resolution: 1.5 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 | 1x82.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x82.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 1x82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x82_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 1x82_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 1x82_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1x82_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/1x82 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/1x82 | HTTPS FTP |
-Related structure data
Related structure data | 1x7nC 1x8eC 1plz 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 | The biological dimer is built by 180 degree rotation around the y axis |
-Components
#1: Protein | Mass: 21871.107 Da / Num. of mol.: 1 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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#2: Sugar | ChemComp-PA5 / |
#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: 1.8 Å3/Da / Density % sol: 31.2 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M tri-sodium citrate, 50mM 5-phospho-D-arabinonate, 100mM MnCl2, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.89843 / Wavelength: 0.89843 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 25, 2003 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89843 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→21 Å / Num. all: 28461 / Num. obs: 26896 / % possible obs: 94.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 1.85 / Num. unique all: 1731 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: 1PLZ 1plz Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.737 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.085 / 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: 23.687 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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