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- PDB-1tzc: Crystal structure of phosphoglucose/phosphomannose isomerase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tzc | ||||||
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Title | Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with 5-phosphoarabinonate | ||||||
![]() | glucose-6-phosphate isomerase, conjectural![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. | ||||||
![]() | ![]() Title: A novel phosphoglucose/phosphomannose isomease 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological unit is a dimer. The asymmetric unit is a dimer. |
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Components
#1: Protein | ![]() Mass: 33590.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8ZWV0, ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Sugar | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 1.45→36 Å / Num. all: 97954 / Num. obs: 97954 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 1.6 / Num. unique all: 9407 / Rsym value: 0.462 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure![]() Starting model: NATIVE STRUCTURE Resolution: 1.45→36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.075 / SU ML: 0.041 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.068 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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