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Yorodumi- PDB-2gc3: The crystal structure of phosphoglucose isomerase from Pyrococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gc3 | ||||||
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Title | The crystal structure of phosphoglucose isomerase from Pyrococcus furiosus in complex with mannose 6-phosphate and zinc | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / cupin / phosphoglucose isomerase / mannose 6-phosphate | ||||||
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: 2.1 Å | ||||||
Authors | Berrisford, J.M. / Rice, D.W. / Baker, P.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase Authors: Berrisford, J.M. / Hounslow, A.M. / Akerboom, J. / Hagen, W.R. / Brouns, S.J. / van der Oost, J. / Murray, I.A. / Michael Blackburn, G. / Waltho, J.P. / 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 | 2gc3.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gc3.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/2gc3 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/2gc3 | HTTPS FTP |
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-Related structure data
Related structure data | 2gc0C 2gc1C 2gc2C 1x8eS 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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-Components
#1: Protein | Mass: 21378.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: pgiA / Plasmid: pLUW557 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P83194, glucose-6-phosphate isomerase #2: Chemical | #3: Sugar | #4: 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: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.05 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 20% PEG monoethyl ether 2000, 5mM ZnCl2, 5mM mannose 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 29, 2005 / Details: Osmic Varimax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→74.835 Å / Num. all: 23477 / Num. obs: 23477 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2 / Num. measured all: 22308 / Num. unique all: 3361 / Num. unique obs: 3361 / Rsym value: 0.366 / % possible all: 100 |
-Phasing
Phasing MR | Rfactor: 0.42 / Cor.coef. Fo:Fc: 0.597
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X8E Resolution: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.066 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.196 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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