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Yorodumi- PDB-5m38: Structure of the TagL peptidoglycan binding domain from EAEC T6SS -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m38 | ||||||
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Title | Structure of the TagL peptidoglycan binding domain from EAEC T6SS | ||||||
Components | OmpA family protein | ||||||
Keywords | SUGAR BINDING PROTEIN / T6SS TagL Peptidoglycan binding domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Cambillau, C. / Nguyen, V.S. / Spinelli, S. / Cascales, E. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Structure of the TagL peptidoglycan binding domain from EAEC T6SS Authors: Cambillau, C. / Nguyen, V.S. / Cascales, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m38.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m38.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m38_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 5m38_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 5m38_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5m38_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m38 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m38 | HTTPS FTP |
-Related structure data
Related structure data | 3td5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15093.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACU81_04615 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0P7P0J8, UniProt: D3GUV9*PLUS #2: 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: 4.36 Å3/Da / Density % sol: 71.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: mixing protein solution (5 mg/ml) with 0.1 M imidazole pH 6.5, 1.2 M NaAc PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.1 Å / Num. obs: 25065 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 97.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.6→2.71 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.53 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TD5 Resolution: 2.6→45.1 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.199
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Displacement parameters | Biso mean: 85.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.434 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→45.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 13
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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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