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Yorodumi- PDB-5f1m: Crystal structure of Serine/threonine phosphatase Stp1 from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f1m | |||||||||
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Title | Crystal structure of Serine/threonine phosphatase Stp1 from Staphylococcus aureus | |||||||||
Components | Phosphorylated protein phosphatasePhosphorylation | |||||||||
Keywords | HYDROLASE / Serine/threonine phosphatase 1 | |||||||||
Function / homology | Function and homology information myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.322 Å | |||||||||
Authors | Zheng, W.H. / Wang, T. / Li, Z.G. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Chem Biol / Year: 2016 Title: Structure-Based Identification of a Potent Inhibitor Targeting Stp1-Mediated Virulence Regulation in Staphylococcus aureus Authors: Zheng, W. / Cai, X. / Xie, M. / Liang, Y. / Wang, T. / Li, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f1m.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f1m.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1m ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1m | HTTPS FTP |
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-Related structure data
Related structure data | 2pk0S 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
#1: Protein | Mass: 30646.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: prpC, AS858_01330, BN1321_240063, EQ80_005655, ER12_005650, ERS093009_00664 Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 plysS References: UniProt: Q9RL81, protein-serine/threonine phosphatase | ||
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#2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15%PEG4000, 200mM MgCl2, 100mM Tris, 0.5mM MnCl2 / PH range: 8.2-8.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 31, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→38.77 Å / Num. obs: 11662 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.22 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.072 / Rrim(I) all: 0.192 / Net I/σ(I): 8.2 / Num. measured all: 80708 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PK0 Resolution: 2.322→32.114 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.37 / 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 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.18 Å2 / Biso mean: 43.9101 Å2 / Biso min: 17.25 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.322→32.114 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: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 48.9257 Å / Origin y: 96.1253 Å / Origin z: 183.1176 Å
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Refinement TLS group | Selection details: chain 'A' |