+Open data
-Basic information
Entry | Database: PDB / ID: 4rx6 | ||||||
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Title | Structure of B. subtilis GlnK-ATP complex to 2.6 Angstrom | ||||||
Components | Nitrogen regulatory PII-like protein | ||||||
Keywords | TRANSCRIPTION / PII protein | ||||||
Function / homology | Function and homology information regulation of nitrogen utilization / enzyme regulator activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5994 Å | ||||||
Authors | Schumacher, M.A. / Cuthbert, B. / Tonthat, N. / Chinnam, N.G. / Whitfill, T. | ||||||
Citation | Journal: Genes Dev. / Year: 2015 Title: Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis. Authors: Schumacher, M.A. / Chinnam, N.B. / Cuthbert, B. / Tonthat, N.K. / Whitfill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rx6.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rx6.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/4rx6 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rx6 | HTTPS FTP |
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-Related structure data
Related structure data | 4r22C 4r24C 4r25SC 4r4eC 4s0rC 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: 13401.415 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: nrgB, BSU36520 / Plasmid: pET15-b / Production host: Escherichia coli (E. coli) / References: UniProt: Q07428 #2: Chemical | #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: 2.97 Å3/Da / Density % sol: 58.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.599→44.7 Å / Num. all: 15175 / Num. obs: 14872 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R25 Resolution: 2.5994→44.687 Å / FOM work R set: 0.7556 / SU ML: 0.49 / σ(F): 0 / Phase error: 30.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.994 Å2 / ksol: 0.348 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.88 Å2 / Biso mean: 50.63 Å2 / Biso min: 23.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5994→44.687 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: 10
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