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Yorodumi- PDB-1x9i: Crystal structure of Crystal structure of phosphoglucose/phosphom... -
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-Basic information
Entry | Database: PDB / ID: 1x9i | ||||||
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Title | Crystal structure of Crystal structure of phosphoglucose/phosphomannose phosphoglucose/phosphomannoseisomerase from Pyrobaculum aerophilum in complex with glucose 6-phosphate | ||||||
Components | glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / enzyme / crenarchaeon / hyperthermophile / PGI superfamily / glucose 6-phosphate | ||||||
Function / homology | Function and homology information mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative metabolic process / carbohydrate derivative binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 1.16 Å | ||||||
Authors | Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from Pyrobaculum aerophilum: a subtle difference between distantly related enzymes. Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. #1: Journal: To be published Title: A novel phosphoglucose isomerase/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16 A resolution Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray diffraction analysis of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x9i.cif.gz | 262.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x9i.ent.gz | 212.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x9i ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x9i | HTTPS FTP |
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-Related structure data
Related structure data | 1x9hC 1tzbS 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 unit is a dimer. The asymmetric unit is a dimer. |
-Components
#1: Protein | Mass: 33590.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: PAE1610 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: GenBank: 18312750, UniProt: Q8ZWV0*PLUS, glucose-6-phosphate isomerase, mannose-6-phosphate isomerase #2: Chemical | #3: Chemical | #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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→36 Å / Num. all: 176109 / Num. obs: 176109 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.16→1.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4 / Num. unique all: 15133 / Rsym value: 0.233 / % possible all: 77.5 |
-Processing
Software |
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Refinement | Method to determine structure: refinement Starting model: pdb entry 1tzb Resolution: 1.16→36 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.886 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.014 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.19 Å / Total num. of bins used: 20
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