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Yorodumi- PDB-3fav: Structure of the CFP10-ESAT6 complex from Mycobacterium tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fav | ||||||
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Title | Structure of the CFP10-ESAT6 complex from Mycobacterium tuberculosis | ||||||
Components |
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Keywords | VIRAL PROTEIN / Complex / Operon structure / Four-helical-bundle / Coiled-coil / WXG-motif / Mycobacterium tuberculosis / secreted / secretion system / adaptor protein / proposed virulent factor | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated perturbation of host signal transduction pathway / protein secretion by the type VII secretion system / Manipulation of host energy metabolism / host cell surface binding / host cell endoplasmic reticulum / host cell membrane / : / peptidoglycan-based cell wall / Modulation by Mtb of host immune system ...symbiont-mediated suppression of host T-cell mediated immune response / symbiont-mediated perturbation of host signal transduction pathway / protein secretion by the type VII secretion system / Manipulation of host energy metabolism / host cell surface binding / host cell endoplasmic reticulum / host cell membrane / : / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / host cell surface / membrane => GO:0016020 / host cell plasma membrane / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Poulsen, C. / Holton, S.J. / Wilmanns, M. / Song, Y.H. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern. Authors: Poulsen, C. / Panjikar, S. / Holton, S.J. / Wilmanns, M. / Song, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fav.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fav.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fav_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 3fav_full_validation.pdf.gz | 471.2 KB | Display | |
Data in XML | 3fav_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3fav_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3fav ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3fav | HTTPS FTP |
-Related structure data
Related structure data | 3gvmC 3gwkC 1wa8S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10873.819 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct contained the entire protein encoding region of the CFP10-ESAT6 operon including its intergenic region Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxB / Plasmid details: modified pSD26 vector / Plasmid: pMyNT / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): MC2 155 / References: UniProt: P0A566, UniProt: P9WNK5*PLUS #2: Protein | Mass: 9777.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct contained the entire protein encoding region of the CFP10-ESAT6 operon including its intergenic region Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxA / Plasmid details: modified pSD26 vector / Plasmid: pMyNT / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): MC2 155 / References: UniProt: P0A564, UniProt: P9WNK7*PLUS #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-IMD / | #5: 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: 1.94 Å3/Da / Density % sol: 36.66 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 33% (v/v) PEG 600, 200mM zinc acetate, 100mM imidazol pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 18161 / Num. obs: 17336 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.35 % / Biso Wilson estimate: 30.407 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.065 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 2149 / Num. unique all: 1333 / Num. unique obs: 978 / Rsym value: 0.261 / % possible all: 73.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WA8 Resolution: 2.15→19.858 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.847 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
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Solvent computation | Bsol: 61.173 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.54 Å2 / Biso mean: 30.573 Å2 / Biso min: 11.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.858 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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