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Yorodumi- PDB-1ko7: X-ray structure of the HPr kinase/phosphatase from Staphylococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ko7 | ||||||
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Title | X-ray structure of the HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution | ||||||
Components | Hpr kinase/phosphatase | ||||||
Keywords | TRANSFERASE / HYDROLASE / Protein kinase / phosphotransfer / protein phosphatase / dual activity / product / substrate | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / regulation of carbohydrate metabolic process / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphorelay sensor kinase activity / protein serine/threonine/tyrosine kinase activity / carbohydrate metabolic process / protein serine/threonine kinase activity / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus xylosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Marquez, J.A. / Hasenbein, S. / Koch, B. / Fieulaine, S. / Nessler, S. / Hengstenberg, W. / Scheffzek, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 A resolution: Mimicking the product/substrate of the phospho transfer reactions. Authors: Marquez, J.A. / Hasenbein, S. / Koch, B. / Fieulaine, S. / Nessler, S. / Russell, R.B. / Hengstenberg, W. / Scheffzek, K. | ||||||
History |
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Remark 600 | HETEROGEN Two phosphate ions in the P-loop regions mimic the substrate/product state of the phospho ...HETEROGEN Two phosphate ions in the P-loop regions mimic the substrate/product state of the phospho transfer reactions |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ko7.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ko7.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ko7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ko7_validation.pdf.gz | 387.8 KB | Display | wwPDB validaton report |
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Full document | 1ko7_full_validation.pdf.gz | 396.4 KB | Display | |
Data in XML | 1ko7_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1ko7_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1ko7 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1ko7 | HTTPS FTP |
-Related structure data
Related structure data | 1jb1S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biologycally relevant structure is an hexamer formed by three equivalent dimers that lay in adjacent asymmetric units. Symmop 2, Shift -1-1 0 Symmop 3, Shift 0-1 0 |
-Components
#1: Protein | Mass: 35373.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus xylosus (bacteria) / Gene: HPRK / Plasmid: pET11a (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) (Stratagene) References: UniProt: Q9S1H5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M SODIUM-POTASSIUM PHOSPHATE PH 7.6, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.99867 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2001 / Details: Toroidal mirror |
Radiation | Monochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99867 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→64.9 Å / Num. obs: 62908 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Rsym value: 0.084 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.338 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 381615 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 99.8 % / Num. unique obs: 4551 / Num. measured obs: 25052 / Rmerge(I) obs: 0.374 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1jb1 Resolution: 1.95→64.9 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 46.7021 Å2 / ksol: 0.380427 e/Å3 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→64.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.226 / Lowest resolution: 50 Å / Num. reflection obs: 62899 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237 |