+Open data
-Basic information
Entry | Database: PDB / ID: 3rx9 | ||||||
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Title | 3D structure of SciN from an Escherichia coli Patotype | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | LIPID BINDING PROTEIN / transthyretin (1sn5) fold / lipoprotein / T6SS assembly / SciS | ||||||
Function / homology | Type VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / Type VI secretion system lipoprotein TssJ Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Felisberto-Rodrigues, C. / Durand, E. / Aschtgen, M.-S. / Blangy, S. / Ortiz-Lombardia, M. / Douzy, B. / Cambillau, C. / Cascales, E. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Towards a Structural Comprehension of Bacterial Type VI Secretion Systems: Characterization of the TssJ-TssM Complex of an Escherichia coli Pathovar. Authors: Felisberto-Rodrigues, C. / Durand, E. / Aschtgen, M.S. / Blangy, S. / Ortiz-Lombardia, M. / Douzi, B. / Cambillau, C. / Cascales, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rx9.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rx9.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rx9_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 3rx9_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 3rx9_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3rx9_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/3rx9 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/3rx9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16975.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 55989 / EAEC / Gene: EC55989_3320, NC_011748.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7LFS8 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: mixing 300 nL protein at 8mg/mL with 100 nL 2.2 M AmSO4, 0.2 M Na+-thiocyanate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2011 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→45 Å / Num. all: 35308 / Num. obs: 35308 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.35→1.39 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.8 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CsI SAD crystal structure Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.275 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 19.15 Å2
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Refine analyze | Luzzati coordinate error free: 0.045 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -17.3791 Å / Origin y: 36.3314 Å / Origin z: -4.3242 Å
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