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Yorodumi- PDB-3cag: Crystal structure of the oligomerization domain hexamer of the ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cag | ||||||
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Title | Crystal structure of the oligomerization domain hexamer of the arginine repressor protein from Mycobacterium tuberculosis in complex with 9 arginines. | ||||||
Components | Arginine repressor | ||||||
Keywords | DNA BINDING PROTEIN / L-Arginine repressor / oligomerization domain / core / alpha/beta topology / TBSGC / Structural Genomics / TB Structural Genomics Consortium / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative | ||||||
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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cag.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cag.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cag_validation.pdf.gz | 486.3 KB | Display | wwPDB validaton report |
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Full document | 3cag_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 3cag_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3cag_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3cag ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3cag | HTTPS FTP |
-Related structure data
Related structure data | 2zfzSC 3bueC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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. ACCORDING TO AUTHORS, THE THREE ADDITIONAL LIGANDS (ARG 400) MAY BE RANDOMLY DISTRIBUTED BETWEEN BIOMOLECULES 2 AND 3. |
-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.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: argR, ahrC, Rv1657, MT1695, MTCY06H11.22 / Plasmid: pGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS #2: Chemical | ChemComp-ARG / #3: 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: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG 10000, 0.1M Hepes pH 7.0, 0.2M L-arginine, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.10552 Å |
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: 1.10552 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 36125 / Num. obs: 36125 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3141 / Rsym value: 0.422 / % possible all: 84.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZFZ Resolution: 1.9→42.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.942 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.15 / 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: 23.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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