+Open data
-Basic information
Entry | Database: PDB / ID: 4r25 | ||||||
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Title | Structure of B. subtilis GlnK | ||||||
Components | Nitrogen regulatory PII-like protein | ||||||
Keywords | TRANSCRIPTION / PII family member / nitrogen regulation / TnrA | ||||||
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 / Resolution: 2.5193 Å | ||||||
Authors | Schumacher, M.A. | ||||||
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 | 4r25.cif.gz | 35.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r25.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r25 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r25 | HTTPS FTP |
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-Related structure data
Related structure data | 4r22C 4r24C 4r4eC 4rx6C 4s0rC 2z0gS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12661.552 Da / Num. of mol.: 1 / Fragment: GlnK, B. subtilis Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: nrgB, BSU36520 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07428 | ||
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#2: Chemical | ChemComp-ZN / #3: 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: 3.19 Å3/Da / Density % sol: 61.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% Peg 8000, 0.1 M MES, 0.1 M zinc acetate, pH 6.5, 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 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.519→63.1 Å / Num. all: 5770 / Num. obs: 5695 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 14.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2z0g Resolution: 2.5193→24.485 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 25.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.654 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5193→24.485 Å
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Refine LS restraints |
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LS refinement shell |
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