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Yorodumi- PDB-8gmx: Crystal structure of pilin-specific sortase SrtC2 from Lactobacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gmx | ||||||
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Title | Crystal structure of pilin-specific sortase SrtC2 from Lactobacillus rhamnosus GG | ||||||
Components | Class C sortase | ||||||
Keywords | HYDROLASE / Pilin-specific sortase / cysteine-transpeptidase / pilus assembly / Ligilactobacillus rhamnosus GG / pilus / probiotics | ||||||
Function / homology | Sortase C / Sortase family / Sortase domain superfamily / Sortase domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / membrane / Class C sortase Function and homology information | ||||||
Biological species | Lacticaseibacillus rhamnosus GG (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Das, S. / Megta, A.K. / Pratap, S. / Krishnan, V. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of pilin-specific sortase SrtC2 from Lactobacillus rhamnosus GG Authors: Das, S. / Megta, A.K. / Pratap, S. / Krishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gmx.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmx.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gmx_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 8gmx_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 8gmx_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 8gmx_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmx ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmx | HTTPS FTP |
-Related structure data
Related structure data | 7cg9S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17282.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lacticaseibacillus rhamnosus GG (bacteria) Strain: ATCC 53103 / LMG 18243 / GG / Gene: GM657_11825, LRHM_2278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7S7JH80 |
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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: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.05 M Citric acid, 0.05 M BIS-TRIS propane pH 5.0, 16% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 2.604→34.814 Å / Num. obs: 4625 / % possible obs: 83.2 % / Redundancy: 8.1 % / CC1/2: 0.992 / Rpim(I) all: 0.077 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.604→2.68 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 231 / CC1/2: 0.415 / Rpim(I) all: 0.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CG9 Resolution: 2.61→34.81 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→34.81 Å
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Refine LS restraints |
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LS refinement shell |
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