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Yorodumi- PDB-7jqe: Structure of an extracellular fragment of EsaA from Streptococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jqe | ||||||
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Title | Structure of an extracellular fragment of EsaA from Streptococcus gallolyticus | ||||||
Components | ESAT-6/WXG100 secretion system protein | ||||||
Keywords | PROTEIN TRANSPORT / Bacterial type VII secretion system / bacterial toxin transport / membrane protein | ||||||
Function / homology | Type VII secretion system EsaA / membrane => GO:0016020 / plasma membrane / ESAT-6/WXG100 secretion system protein Function and homology information | ||||||
Biological species | Streptococcus gallolyticus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Klein, T.A. / Grebenc, D.W. / Kim, Y. / Whitney, J.C. | ||||||
Citation | Journal: Structure / Year: 2021 Title: Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA. Authors: Klein, T.A. / Grebenc, D.W. / Gandhi, S.Y. / Shah, V.S. / Kim, Y. / Whitney, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jqe.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jqe.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 7jqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/7jqe ftp://data.pdbj.org/pub/pdb/validation_reports/jq/7jqe | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 66067.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus gallolyticus (strain ATCC 43143 / F-1867) (bacteria) Strain: ATCC 43143 / F-1867 / Gene: esaA, SGGB_0524 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: F5WZF6 | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M MgCl2, 0.1M Tris-HCl pH 7.0, 10% (w/v) PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→55.3 Å / Num. obs: 29568 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 51.38 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.069 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1 / Num. unique obs: 1310 / CC1/2: 0.513 / Rpim(I) all: 0.644 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→41.37 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7526 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→41.37 Å
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Refine LS restraints |
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LS refinement shell |
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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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