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- PDB-2zfz: Crystal structure of the C-terminal domain hexamer of ArgR from M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zfz | ||||||
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Title | Crystal structure of the C-terminal domain hexamer of ArgR from Mycobacterium tuberculosis in complex with arginine | ||||||
![]() | Arginine repressor | ||||||
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Function / homology | ![]() arginine biosynthetic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis. Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.3 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bueC ![]() 3cagC ![]() 1b4bS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | AUTHORS STATE THAT THE ASYMMETRIC UNIT CONTAINS ONE HEXAMER THAT IS A DIMER OF TRIMERS. EITHER HEXAMER OR TRIMER MIGHT BE THE BIOLOGICAL UNIT. |
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Components
#1: Protein | Mass: 8137.206 Da / Num. of mol.: 6 / Fragment: C-terminal domain: Residues 92-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ARG / ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 10000, 0.1 M Tris-HCl, 0.1 M Guanidine-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→61.9 Å / Num. all: 41086 / Num. obs: 41086 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 17.79 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.03 / Rsym value: 0.8 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1B4B, poly-alanine model Resolution: 1.85→43.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.248 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.233 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Total num. of bins used: 20
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