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Yorodumi- PDB-5nod: PASTA subunit 4 of Streptococcus pneumoniae STKP crystallized wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nod | ||||||
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Title | PASTA subunit 4 of Streptococcus pneumoniae STKP crystallized with PEG and succinate | ||||||
Components | Serine/threonine-protein kinase StkP | ||||||
Keywords | TRANSFERASE / PASTA / extracellular domain / Ser/Thr kinase / Streptococcus pneumoniae | ||||||
Function / homology | Function and homology information protein serine/threonine kinase activity => GO:0004674 / division septum assembly / regulation of cell shape / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Galisson, F. / Gueguen-Chaignon, V. / Gouet, P. / Grangeasse, C. / Zucchini, L. | ||||||
Citation | Journal: Nat Microbiol / Year: 2018 Title: PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae. Authors: Zucchini, L. / Mercy, C. / Garcia, P.S. / Cluzel, C. / Gueguen-Chaignon, V. / Galisson, F. / Freton, C. / Guiral, S. / Brochier-Armanet, C. / Gouet, P. / Grangeasse, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nod.cif.gz | 28.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nod.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nod_validation.pdf.gz | 411.3 KB | Display | wwPDB validaton report |
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Full document | 5nod_full_validation.pdf.gz | 411.3 KB | Display | |
Data in XML | 5nod_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 5nod_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5nod ftp://data.pdbj.org/pub/pdb/validation_reports/no/5nod | HTTPS FTP |
-Related structure data
Related structure data | 3ouvS 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: 9084.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria) Gene: stkP, pkn2, spr1577 / Production host: Escherichia coli (E. coli) References: UniProt: Q8DNS0, non-specific serine/threonine protein kinase |
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#2: 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: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15% PEG3350 0,1M Succinate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.774 Å / Num. obs: 7718 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.386 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 / Rsym value: 0.042 / Χ2: 0.97 / Net I/av σ(I): 43.06 / Net I/σ(I): 42.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 11.773 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 4.67 / Num. unique obs: 550 / CC1/2: 0.943 / Rpim(I) all: 0.164 / Rrim(I) all: 0.603 / Rsym value: 0.577 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OUV Resolution: 1.9→19.774 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 69.94 Å2 / Biso mean: 35.1098 Å2 / Biso min: 18.84 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→19.774 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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