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Yorodumi- PDB-1b0z: The crystal structure of phosphoglucose isomerase-an enzyme with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b0z | ||||||
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Title | The crystal structure of phosphoglucose isomerase-an enzyme with autocrine motility factor activity in tumor cells | ||||||
Components | PROTEIN (PHOSPHOGLUCOSE ISOMERASE) | ||||||
Keywords | ISOMERASE / PHOSPHOGLUCOSE ISOMERASE / AUTOCRINEFACTOR / NEUROLEUKIN / CRYSTALLOGRAPHY MOTILITY | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.3 Å | ||||||
Authors | Sun, Y.-J. / Chou, C.-C. / Chen, W.-S. / Meng, M. / Hsiao, C.-D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The crystal structure of phosphoglucose isomerase/autocrine motility factor/neuroleukin complexed with its carbohydrate phosphate inhibitors suggests its substrate/receptor recognition Authors: Chou, C.-C. / Sun, Y.-J. / Meng, M. / Hsiao, C.-D. #1: Journal: J.Mol.Biol. / Year: 1977 Title: Crystallographic Structure Analysis of Glucose-6-Phosphate Isomerase at 3.5 A Resolution Authors: Shaw, P.J. / Muirhead, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b0z.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0z.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0z ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50202.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: PGIB / Plasmid: PMMB67EH / Production host: Escherichia coli (E. coli) / Strain (production host): DF2145 / References: UniProt: P13376, glucose-6-phosphate isomerase |
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#2: 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: 3.08 Å3/Da / Density % sol: 60 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION FROM 4-UL DROPLETS OF PROTEIN SOLUTION (15 MG/ML) IN 50 MM PHOSPHATE BUFFER (PH7.0) AND 0.2 M AMMONIUM PHOSPHATE AGAINST A RESERVOIR OF ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION FROM 4-UL DROPLETS OF PROTEIN SOLUTION (15 MG/ML) IN 50 MM PHOSPHATE BUFFER (PH7.0) AND 0.2 M AMMONIUM PHOSPHATE AGAINST A RESERVOIR OF THE ABOVE BUFFER CONTAINING 0.4M AMMONIUM PHOSPHATE., VAPOR DIFFUSION, HANGING DROP |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 25, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.7 Å / Num. obs: 24024 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.11 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.3→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |