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Yorodumi- PDB-1f9n: CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f9n | ||||||
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Title | CRYSTAL STRUCTURE OF AHRC, THE ARGININE REPRESSOR/ACTIVATOR PROTEIN FROM BACILLUS SUBTILIS | ||||||
Components | ARGININE REPRESSOR/ACTIVATOR PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / WINGED-HELIX-TURN-HELIX / ARGININE REPRESSOR | ||||||
Function / homology | Function and homology information arginine catabolic process to ornithine / arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Dennis, C.A. / Glykos, N.M. / Parsons, M.R. / Phillips, S.E.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Authors: Dennis C, C.A. / Glykos, N.M. / Parsons, M.R. / Phillips, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9n.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9n.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 1f9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9n ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9n | HTTPS FTP |
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-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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Details | The biological assembly is a hexamer with 32 symmetry. The hexamer is formed by a dimer of trimers. |
-Components
#1: Protein | Mass: 16854.479 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P17893 #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: 2.92 Å3/Da / Density % sol: 57.87 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: PEG 4000, ammonium sulphate, phosphate buffer, protease inhibitors (PMSF, TPCK) in isopropanol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 44888 / Num. obs: 28055 / % possible obs: 88.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 1.6 % / Biso Wilson estimate: 66.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.14 / Num. unique all: 4440 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Resolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.87 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.27 / Num. reflection Rwork: 4440 |