+Open data
-Basic information
Entry | Database: PDB / ID: 1ble | ||||||
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Title | PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM | ||||||
Components | FRUCTOSE PERMEASE | ||||||
Keywords | PHOSPHOTRANSFERASE / SUGAR TRANSPORT | ||||||
Function / homology | Function and homology information protein-Npi-phosphohistidine-D-fructose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å | ||||||
Authors | Schauder, S. / Schirmer, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of the IIB subunit of a fructose permease (IIBLev) from Bacillus subtilis. Authors: Schauder, S. / Nunn, R.S. / Lanz, R. / Erni, B. / Schirmer, T. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Levanase Operon of Bacillus Subtilis Includes a Fructose-Specific Phosphotransferase System Regulating the Expression of the Operon Authors: Martin-Verstraete, I. / Debarbouille, M. / Klier, A. / Rapoport, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ble.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ble.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ble.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ble_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 1ble_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 1ble_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1ble_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/1ble ftp://data.pdbj.org/pub/pdb/validation_reports/bl/1ble | 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: 18241.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: WA2127 AND D41 / Gene: LEVE / Plasmid: PRL1 / Production host: Bacillus subtilis (bacteria) References: UniProt: P26380, protein-Npi-phosphohistidine-sugar phosphotransferase |
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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: 2.79 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 2, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 4889 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.288 / % possible all: 96.7 |
Reflection shell | *PLUS % possible obs: 96.7 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: EXCEPT FOR THE ACTIVE LOOP RESIDUE PHE 13, ALL MAIN CHAIN ATOMS ARE WITHIN THE ALLOWED REGIONS OF THE RAMACHANDRAN PLOT.
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Displacement parameters | Biso mean: 64.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.03 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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