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Yorodumi- PDB-1b4a: STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b4a | |||||||||
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Title | STRUCTURE OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS | |||||||||
Components | ARGININE REPRESSOR | |||||||||
Keywords | REPRESSOR / ARGININE / HELIX TURN HELIX | |||||||||
Function / homology | Function and homology information arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Ni, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure of the arginine repressor from Bacillus stearothermophilus. Authors: Ni, J. / Sakanyan, V. / Charlier, D. / Glansdorff, N. / Van Duyne, G.D. #1: Journal: Thesis, University of Pennsylvania / Year: 1998 Title: The Crystal Structure of Arginine Repressor Authors: Ni, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b4a.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4a.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b4a_validation.pdf.gz | 403.2 KB | Display | wwPDB validaton report |
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Full document | 1b4a_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 1b4a_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 1b4a_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4a ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4a | HTTPS FTP |
-Related structure data
Related structure data | 1b4bC 1xxcS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 16809.545 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: O31408 #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: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9 |
Detector | Detector: CCD / Date: Dec 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32 Å / Num. obs: 35454 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.064 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.201 / % possible all: 100 |
Reflection | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XXC Resolution: 2.5→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: 2.5→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: 2.5→2.6 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: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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