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Yorodumi- PDB-3roj: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3roj | ||||||
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Title | D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 | ||||||
Components | D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase | ||||||
Keywords | HYDROLASE / fructose-1 / 6-/sedoheptulose-1 / 7-bisphosphatase | ||||||
Function / homology | Function and homology information sedoheptulose-bisphosphatase / sedoheptulose-bisphosphatase activity / glycerol metabolic process / reductive pentose-phosphate cycle / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / metal ion binding Similarity search - Function | ||||||
Biological species | Synechocystis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hu, X. / Hui, D. / Lingling, F. / Jian, W. | ||||||
Citation | Journal: To be Published Title: New insights into the structural and interactional basis for a promising route towards fructose-1,6-/sedoheptulose-1,7-bisphosphatases controlling Authors: Hu, X. / Lingling, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3roj.cif.gz | 297.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3roj.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 3roj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/3roj ftp://data.pdbj.org/pub/pdb/validation_reports/ro/3roj | HTTPS FTP |
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-Related structure data
Related structure data | 3rplC 3d1rS C: citing same article (ref.) 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40653.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: slr2094 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P73922, fructose-bisphosphatase, sedoheptulose-bisphosphatase |
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-Non-polymers , 6 types, 934 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-AMP / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / | #7: 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: 3.12 Å3/Da / Density % sol: 60.56 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 1.6M Ammonium Sulfate, 7-9% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | |||||||||||||||||||||
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Aug 12, 2010 | |||||||||||||||||||||
Radiation | Monochromator: multilayer optics / 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→25.95 Å / Num. all: 87598 / Num. obs: 87598 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.7 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D1R Resolution: 2.3→25.542 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8723 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.13 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.81 Å2 / Biso mean: 30.8998 Å2 / Biso min: 0 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.542 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: 30
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