+Open data
-Basic information
Entry | Database: PDB / ID: 2fez | ||||||
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Title | Mycobacterium tuberculosis EmbR | ||||||
Components | Probable regulatory protein embR | ||||||
Keywords | TRANSCRIPTION / transcriptional regulator / winged-helix / tetratricopeptide repeat / beta-sandwich | ||||||
Function / homology | Function and homology information cell wall / phosphorelay signal transduction system / peptidoglycan-based cell wall / GTPase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Futterer, K. / Alderwick, L.J. / Besra, G.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Molecular structure of EmbR, a response element of Ser/Thr kinase signaling in Mycobacterium tuberculosis Authors: Alderwick, L.J. / Molle, V. / Kremer, L. / Cozzone, A.J. / Dafforn, T.R. / Besra, G.S. / Futterer, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fez.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fez.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/2fez ftp://data.pdbj.org/pub/pdb/validation_reports/fe/2fez | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41988.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: embR / Plasmid: pET23c / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P66799, UniProt: P9WGJ9*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na-Hepes, pH 7.5, 15% PEG 4000, 0.2 M magnesium choride, 5 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→44.4 Å / Num. all: 31575 / Num. obs: 31575 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.6 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4565 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→42 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.441 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.149 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 25.521 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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