+Open data
-Basic information
Entry | Database: PDB / ID: 4jmp | ||||||
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Title | Crystal structure of the chimerical protein CapA2B2 | ||||||
Components | C-terminal fragment of CapA, Protein tyrosine kinase | ||||||
Keywords | TRANSFERASE / Rossmann fold / tyrosine kinase | ||||||
Function / homology | Function and homology information lipopolysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Olivares-Illana, V. / Morera, S. / Grangeasse, C. / Nessler, S. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Comparative analysis of the Tyr-kinases CapB1 and CapB2 fused to their cognate modulators CapA1 and CapA2 from Staphylococcus aureus Authors: Gruszczyk, J. / Olivares-Illana, V. / Nourikyan, J. / Fleurie, A. / Bechet, E. / Gueguen-Chaignon, V. / Freton, C. / Aumont-Nicaise, M. / Morera, S. / Grangeasse, C. / Nessler, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jmp.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jmp.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 4jmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jmp_validation.pdf.gz | 413.2 KB | Display | wwPDB validaton report |
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Full document | 4jmp_full_validation.pdf.gz | 413.8 KB | Display | |
Data in XML | 4jmp_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4jmp_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/4jmp ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jmp | HTTPS FTP |
-Related structure data
Related structure data | 4jlvC 3bfvS 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: 29708.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of CapA and Protein tyrosine kinase / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: capA2, capB2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BSA3, UniProt: A8YPQ5 |
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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: 1.93 Å3/Da / Density % sol: 36.29 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG550 MME, 100mM Hepes, 5mM MgCl2, pH 7.5, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 31, 2007 |
Radiation | Monochromator: horizontally diffracting Si(111) monochromator and Pt coated mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→35.6 Å / Num. all: 55233 / Num. obs: 54294 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Biso Wilson estimate: 10.66 Å2 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7988 / Rsym value: 0.551 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BFV Resolution: 1.3→33.046 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8999 / SU ML: 0.12 / σ(F): 1.36 / Phase error: 17.67 / 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: 58.68 Å2 / Biso mean: 15.4318 Å2 / Biso min: 5.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→33.046 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: 20
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