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Yorodumi- PDB-4wmj: Colias eurytheme Phosphoglucose isomerase. Homodimer from 4-5(18)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wmj | ||||||
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Title | Colias eurytheme Phosphoglucose isomerase. Homodimer from 4-5(18) genotype. | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / Glycolysis | ||||||
Function / homology | Function and homology information glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Colias eurytheme (orange sulphur) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Hill, J.A. / Watt, W.B. | ||||||
Citation | Journal: Thesis, Stanford University / Year: 2013 Title: Structure and Function of Phosphoglucose Isomerase In Colias Eurytheme Authors: Hill, J.A. / Watt, W.B. / Jardetzky, T. / Tuljapurkar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wmj.cif.gz | 827.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wmj.ent.gz | 688.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wmj ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wmj | HTTPS FTP |
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-Related structure data
Related structure data | 1u0eS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61938.219 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colias eurytheme (orange sulphur) / Gene: PGI / Production host: Escherichia coli (E. coli) / References: UniProt: G9BZJ0, glucose-6-phosphate isomerase #2: 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: 2.35 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M lithium sulfate, 22% PEG 4000, 0.2M Tris-Cl pH 7.4. |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.19 Å / Num. obs: 270174 / % possible obs: 77.68 % / Redundancy: 2 % / Net I/σ(I): 8.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U0E Resolution: 1.5→41.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.507 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / 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: 18.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→41.19 Å
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Refine LS restraints |
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