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- PDB-1b4b: STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1b4b | ||||||
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Title | STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS | ||||||
![]() | ARGININE REPRESSOR | ||||||
![]() | REPRESSOR / ARGININE / CORE / OLIGOMERIZATION DOMAIN / HELIX TURN HELIX | ||||||
Function / homology | ![]() arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ni, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D. | ||||||
![]() | ![]() Title: Structure of the arginine repressor from Bacillus stearothermophilus. Authors: Ni, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D. #1: ![]() Title: The Crystal Structure of Arginine Repressor Authors: Ni, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.2 KB | Display | ![]() |
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PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.8 KB | Display | ![]() |
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Full document | ![]() | 402.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b4aC ![]() 1xxcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 7640.941 Da / Num. of mol.: 3 / Fragment: OLIGOMERIZATION DOMAIN, L-ARGININE BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 12146 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.052 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.26 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.216 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.216 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XXC Resolution: 2.2→8 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 48 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev position: 1.5 Å / Weight Biso : 1
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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