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Yorodumi- PDB-3fhz: Crystal structure of the arginine repressor from Mycobacterium tu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fhz | ||||||
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Title | Crystal structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and co-repressor, L-arginine | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Mycobacterium tuberculosis / arginine repressor protein / DNA binding / ArgR-operator ternary complex / Structural Genomics / TB structural genomics / TB Structural Genomics Consortium / TBSGC / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Repressor / Transcription / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
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: 3.27 Å | ||||||
Authors | Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine. Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / 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 | 3fhz.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fhz.ent.gz | 196.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/3fhz ftp://data.pdbj.org/pub/pdb/validation_reports/fh/3fhz | HTTPS FTP |
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-Related structure data
Related structure data | 2fzfS 3ereS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Details | The biological unit is the content of the asymmetric unit: arginine repressor hexamer with bound three copies of the DNA operator and arginine molecules |
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 17366.635 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ahrC, argR, MT1695, MTCY06H11.22, Rv1657 / Plasmid: pGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS |
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-DNA chain , 2 types, 6 molecules GIKHJL
#2: DNA chain | Mass: 6166.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 20 oligonucleotide DNA segment 1 #3: DNA chain | Mass: 6098.964 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 20 oligonucleotide DNA segment 2 |
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-Non-polymers , 4 types, 85 molecules
#4: Chemical | ChemComp-ARG / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 2.78 Å3/Da / Density % sol: 55.73 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 100mM Bis-tris, 0.2M KF, 15% Glycerol, 10mM Arginine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.27→50 Å / Num. obs: 24627 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 96.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.27→3.42 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.57 / Num. unique all: 2445 / Rsym value: 0.563 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2FZF, 3ERE Resolution: 3.27→44.339 Å / SU ML: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.592 Å2 / ksol: 0.314 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.27→44.339 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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