+Open data
-Basic information
Entry | Database: PDB / ID: 1knx | ||||||
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Title | HPr kinase/phosphatase from Mycoplasma pneumoniae | ||||||
Components | Probable HPr(Ser) kinase/phosphatase | ||||||
Keywords | transferase/hydrolase / HPr kinase / Hpr kinase/phosphatase / HPrK/P / kinase / phosphatase / P-loop / WALKER A BOX / CATABOLITE REPRESSION / transferase-hydrolase COMPLEX | ||||||
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 | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å | ||||||
Authors | Allen, G.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of HPr Kinase/Phosphatase from Mycoplasma pneumoniae Authors: Allen, G.S. / Steinhauer, K. / Hillen, W. / Stulke, J. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1knx.cif.gz | 360.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1knx.ent.gz | 298.8 KB | Display | PDB format |
PDBx/mmJSON format | 1knx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1knx_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 1knx_full_validation.pdf.gz | 524.2 KB | Display | |
Data in XML | 1knx_validation.xml.gz | 68 KB | Display | |
Data in CIF | 1knx_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1knx ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1knx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35276.969 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Production host: Escherichia coli (E. coli) References: UniProt: P75548, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: 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: 2.9 Å3/Da / Density % sol: 59 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 8000, sodium chloride, magnesium chloride, tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 Details: Steinhauer, K., (2002) Acta Crystallogr., D58, 515. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 0.8856 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 91137 / % possible obs: 97.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.49→2.59 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.418 / % possible all: 94.8 |
Reflection | *PLUS Highest resolution: 2.49 Å / Lowest resolution: 30 Å / Num. measured all: 347151 |
Reflection shell | *PLUS % possible obs: 94.8 % / Rmerge(I) obs: 0.418 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→29.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 225180.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3269 Å2 / ksol: 0.35087 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.49 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |