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Yorodumi- PDB-1xxb: C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xxb | ||||||
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Title | C-TERMINAL DOMAIN OF ESCHERICHIA COLI ARGININE REPRESSOR/ L-ARGININE COMPLEX | ||||||
Components | ARGININE REPRESSOR | ||||||
Keywords | COMPLEX (DNA BINDING PROTEIN/PEPTIDE) / COMPLEX (DNA BINDING PROTEIN-PEPTIDE) / COMPLEX (DNA BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information regulation of arginine biosynthetic process / regulation of arginine catabolic process / plasmid recombination / negative regulation of DNA-templated transcription initiation / positive regulation of DNA-templated transcription initiation / arginine biosynthetic process / arginine binding / cis-regulatory region sequence-specific DNA binding / protein complex oligomerization / transcription regulator complex ...regulation of arginine biosynthetic process / regulation of arginine catabolic process / plasmid recombination / negative regulation of DNA-templated transcription initiation / positive regulation of DNA-templated transcription initiation / arginine biosynthetic process / arginine binding / cis-regulatory region sequence-specific DNA binding / protein complex oligomerization / transcription regulator complex / DNA-binding transcription factor activity / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Van Duyne, G.D. / Ghosh, G. / Maas, W.K. / Sigler, P.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Structure of the oligomerization and L-arginine binding domain of the arginine repressor of Escherichia coli. Authors: Van Duyne, G.D. / Ghosh, G. / Maas, W.K. / Sigler, P.B. #1: Journal: Mol.Microbiol. / Year: 1994 Title: The Arginine Repressor of Escherichia Coli Authors: Maas, W.K. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Nucleotide Sequence of the Argr Gene of Escherichia Coli K-12 and Isolation of its Product, the Arginine Repressor Authors: Lim, D.B. / Oppenheim, J.D. / Eckhardt, T. / Maas, W.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xxb.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xxb.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xxb_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 1xxb_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 1xxb_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1xxb_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/1xxb ftp://data.pdbj.org/pub/pdb/validation_reports/xx/1xxb | HTTPS FTP |
-Related 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: 8351.467 Da / Num. of mol.: 6 / Fragment: INITIATOR MET PLUS C-TERMINAL RESIDUES 80 - 156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Description: T7 PROMOTER SYSTEM (NOVAGEN) / Gene: T7 / Plasmid: PET3A / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6D0 #2: Chemical | ChemComp-ARG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 |
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Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 12971 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Resolution: 2.6→8 Å / σ(I): 3
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Displacement parameters | Biso mean: 48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 12971 / Rfactor all: 0.245 / Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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