[English] 日本語
Yorodumi- PDB-6ihv: Crystal structure of bacterial serine phosphatase bearing R161E m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ihv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bacterial serine phosphatase bearing R161E mutation | ||||||
Components | Phosphorylated protein phosphatase | ||||||
Keywords | HYDROLASE / bacteria / phosphatase / metal binding | ||||||
Function / homology | Function and homology information negative regulation of stress-activated MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / negative regulation of canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of canonical NF-kappaB signal transduction / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yang, C.-G. / yang, T. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Acs Infect Dis. / Year: 2019 Title: Structural Insight into the Mechanism of Staphylococcus aureus Stp1 Phosphatase. Authors: Yang, T. / Liu, T. / Gan, J. / Yu, K. / Chen, K. / Xue, W. / Lan, L. / Yang, S. / Yang, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ihv.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ihv.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ihv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ihv_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ihv_full_validation.pdf.gz | 431.2 KB | Display | |
Data in XML | 6ihv_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6ihv_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ihv ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ihv | HTTPS FTP |
-Related structure data
Related structure data | 6ihlC 6ihrC 6ihsC 6ihtC 6ihuC 6ihwC 5f1mS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30109.582 Da / Num. of mol.: 1 / Mutation: R161E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC9944_01222, RK64_06500, ...Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC9944_01222, RK64_06500, SAMEA1469870_01594, SAMEA1531701_01402 Production host: Escherichia coli (E. coli) References: UniProt: Q9RL81, protein-serine/threonine phosphatase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.67 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH=7.5), 25% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9735 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9735 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 17003 / % possible obs: 91.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→2.01 Å / Rmerge(I) obs: 0.241 / Num. unique obs: 1510 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F1M Resolution: 1.9→29.604 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.62 / Phase error: 20.93
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.604 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|