[English] 日本語
Yorodumi- PDB-7uqw: PCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uqw | ||||||
---|---|---|---|---|---|---|---|
Title | PCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer | ||||||
Components | Cyanophycinase | ||||||
Keywords | HYDROLASE / cyanophycinase / CphB / cyanophycin | ||||||
Function / homology | Function and homology information cyanophycinase / serine-type peptidase activity / protein homodimerization activity / proteolysis Similarity search - Function | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Sharon, I. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2022 Title: The structure of cyanophycinase in complex with a cyanophycin degradation intermediate. Authors: Sharon, I. / Grogg, M. / Hilvert, D. / Schmeing, T.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7uqw.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7uqw.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 7uqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uqw_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7uqw_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7uqw_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 7uqw_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/7uqw ftp://data.pdbj.org/pub/pdb/validation_reports/uq/7uqw | HTTPS FTP |
-Related structure data
Related structure data | 7uqvC 3en0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30117.398 Da / Num. of mol.: 3 Mutation: S132DAP (diaminopropanoate: a modified amino acid) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: cphB, slr2001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73832, cyanophycinase #2: Chemical | ChemComp-7ID / ( #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-ARF / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.4 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.6, 1.65 M ammonium sulfate and 4% formamide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→61.61 Å / Num. obs: 133142 / % possible obs: 99.92 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.18 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 13155 / CC1/2: 0.866 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EN0 Resolution: 1.5→61.61 Å / SU ML: 0.1446 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 17.4545 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→61.61 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|