[English] 日本語
Yorodumi- PDB-2d2v: X-ray structure of the sucrose-phosphatase (SPP) from Synechocyst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d2v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray structure of the sucrose-phosphatase (SPP) from Synechocystis sp.PCC6803 in complex with maltose | |||||||||
Components | hypothetical protein slr0953 | |||||||||
Keywords | HYDROLASE / phosphohydrolase / HAD superfamily / maltose / cyanobacteria | |||||||||
Function / homology | Function and homology information sucrose-phosphate phosphatase / sucrose-phosphate phosphatase activity / sucrose biosynthetic process / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body / Resolution: 2.5 Å | |||||||||
Authors | Fieulaine, S. / Lunn, J.E. / Ferrer, J.-L. | |||||||||
Citation | Journal: Proteins / Year: 2007 Title: Crystal structure of a cyanobacterial sucrose-phosphatase in complex with glucose-containing disaccharides Authors: Fieulaine, S. / Lunn, J.E. / Ferrer, J.-L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d2v.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d2v.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 2d2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d2v_validation.pdf.gz | 788.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2d2v_full_validation.pdf.gz | 790.9 KB | Display | |
Data in XML | 2d2v_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2d2v_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2v ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2v | HTTPS FTP |
-Related structure data
Related structure data | 2b1qC 2b1rC 1tj3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27789.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: spp / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74325, sucrose-phosphate phosphatase |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.8 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: NaFormate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2004 |
Radiation | Monochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 13929 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 13.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: rigid body Starting model: 1tj3 Resolution: 2.5→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|