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Yorodumi- PDB-1koj: Crystal structure of rabbit phosphoglucose isomerase complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1koj | ||||||
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Title | Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / protein - inhibitor complex | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / monosaccharide binding / cytokine activity / gluconeogenesis / glycolytic process / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Arsenieva, D. / Hardre, R. / Salmon, L. / Jeffery, C.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid. Authors: Arsenieva, D. / Hardre, R. / Salmon, L. / Jeffery, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1koj.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1koj.ent.gz | 196.9 KB | Display | PDB format |
PDBx/mmJSON format | 1koj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1koj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1koj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1koj_validation.xml.gz | 52 KB | Display | |
Data in CIF | 1koj_validation.cif.gz | 75.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1koj ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1koj | HTTPS FTP |
-Related structure data
Related structure data | 1dqrS S: Starting model for refinement |
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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: 62696.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Cellular location: Cytoplasmic / Tissue: skeletal muscle / References: UniProt: Q9N1E2, glucose-6-phosphate isomerase #2: Chemical | #3: 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: 2.6 Å3/Da / Density % sol: 52.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14% PEG 8000, 250mM magnesium acetate, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 114 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2000 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 96961 / Num. obs: 96961 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.98 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4 / Num. unique all: 9158 / Rsym value: 0.327 / % possible all: 89 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Num. measured all: 400188 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 89 % / Num. unique obs: 9158 / Rmerge(I) obs: 0.327 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DQR Resolution: 1.9→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / Rfactor all: 0.223 / Rfactor obs: 0.22 / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.9 Å / Rfactor Rfree: 0.335 / % reflection Rfree: 10 % / Rfactor Rwork: 0.307 / Rfactor obs: 0.307 |