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- PDB-3rpl: D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rpl | ||||||
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Title | D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 in complex with FRUCTOSE-1,6-BISPHOSPHATE | ||||||
![]() | (D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7- ...) x 2 | ||||||
![]() | HYDROLASE / fructose-1 / 6-/sedoheptulose-1 / 7-bisphosphatase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hu, X. / Hui, D. / Lingling, F. / Jian, W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.7 KB | Display | ![]() |
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PDB format | ![]() | 232.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 59.7 KB | Display | |
Data in CIF | ![]() | 84.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rojSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7- ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 40637.344 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P73922, fructose-bisphosphatase, sedoheptulose-bisphosphatase #2: Protein | | Mass: 40669.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P73922, fructose-bisphosphatase, sedoheptulose-bisphosphatase |
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-Sugars , 1 types, 4 molecules ![](data/chem/img/FBP.gif)
#4: Sugar | ChemComp-FBP / |
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-Non-polymers , 6 types, 804 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #5: Chemical | ChemComp-AMP / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.15 % |
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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, 10mM FBP, 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 14, 2010 / Details: multilayer optics | |||||||||||||||||||||
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: 2.4→25.72 Å / Num. all: 78184 / Num. obs: 78184 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.4 | |||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ROJ Resolution: 2.4→25.719 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.88 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 19.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.799 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.54 Å2 / Biso mean: 27.4848 Å2 / Biso min: 8.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→25.719 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: 28
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