+Open data
-Basic information
Entry | Database: PDB / ID: 6ihr | ||||||
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Title | Crystal structure of bacterial serine phosphatase with His tag | ||||||
Components | Phosphorylated protein phosphatasePhosphorylation | ||||||
Keywords | HYDROLASE / bacteria / phosphatase / metal binding | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.348 Å | ||||||
Authors | Yang, C.-G. / yang, T. | ||||||
Funding support | China, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ihr.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ihr.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ihr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ihr ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ihr | HTTPS FTP |
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-Related structure data
Related structure data | 6ihlC 6ihsC 6ihtC 6ihuC 6ihvC 6ihwC 5f1mS S: Starting model for refinement C: citing same article (ref.) |
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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: 30137.660 Da / Num. of mol.: 1 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, NCTC10654_01263, NCTC10702_01924, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, ...Gene: prpC, prpC_1, BN1321_240063, BTN44_06615, CSC83_01010, CSC87_08725, EP54_08495, EQ90_08165, ERS072840_01404, NCTC10654_01263, NCTC10702_01924, NCTC11940_01141, NCTC13131_00423, NCTC13196_02843, NCTC13812_01250, NCTC9944_01222, RK64_06500, SAMEA1469870_01594, SAMEA1531701_01402 Production host: Escherichia coli (E. coli) References: UniProt: Q9RL81, protein-serine/threonine phosphatase | ||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: 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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M LiSO4, 0.1 M Tris-HCl (pH=8.0), 30% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9735 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9735 Å / Relative weight: 1 |
Reflection | Resolution: 1.348→29.1 Å / Num. obs: 59431 / % possible obs: 99.3 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 5623 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F1M Resolution: 1.348→29.088 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 15.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.348→29.088 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.8775 Å / Origin y: 12.3855 Å / Origin z: -10.5982 Å
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Refinement TLS group | Selection details: (chain A and resseq -11:245) |