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Yorodumi- PDB-8kg4: Crystal Structure of M- and C-Domains of the shaft pilin LrpA fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kg4 | ||||||
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Title | Crystal Structure of M- and C-Domains of the shaft pilin LrpA from Ligilactobacillus ruminis - orthorhombic form | ||||||
Components | LPXTG-motif cell wall anchor domain protein | ||||||
Keywords | CELL ADHESION / Backbone pilin / isopeptide bond / pili / gut bacteria / probiotic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ligilactobacillus ruminis ATCC 25644 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Prajapati, A. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
Funding support | India, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis. Authors: Prajapati, A. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kg4.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kg4.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 8kg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kg4_validation.pdf.gz | 7 MB | Display | wwPDB validaton report |
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Full document | 8kg4_full_validation.pdf.gz | 7 MB | Display | |
Data in XML | 8kg4_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 8kg4_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/8kg4 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/8kg4 | HTTPS FTP |
-Related structure data
Related structure data | 8kb2C 8kclC 8w5bC 8wb8C C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28740.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A truncated form of Shaft pilin LrpA produced by limited proteolysis with subtilisin Source: (gene. exp.) Ligilactobacillus ruminis ATCC 25644 (bacteria) Gene: HMPREF0542_11612 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: E7FRT5 |
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-Non-polymers , 5 types, 207 molecules
#2: Chemical | ChemComp-IOD / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9803 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9803 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→39.71 Å / Num. obs: 84143 / % possible obs: 99.6 % / Redundancy: 8.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.034 / Rrim(I) all: 0.102 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.2→1.223 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4207 / CC1/2: 0.888 / Rpim(I) all: 0.292 / Rrim(I) all: 0.834 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.115 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 8.752 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→39.71 Å
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Refine LS restraints |
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