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- PDB-5yxg: Crystal structure of C-terminal fragment of SpaD from Lactobacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yxg | ||||||
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Title | Crystal structure of C-terminal fragment of SpaD from Lactobacillus rhamnosus GG generated by limited proteolysis | ||||||
![]() | (Pilus assembly protein) x 2 | ||||||
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Function / homology | Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Pilus assembly protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism. Authors: Chaurasia, P. / Pratap, S. / Palva, A. / von Ossowski, I. / Krishnan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 251.8 KB | Display | ![]() |
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PDB format | ![]() | 199.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yu5SC ![]() 5yxoC ![]() 5z0zC ![]() 5z24C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 184 - 480 / Label seq-ID: 8 - 304
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Components
#1: Protein | Mass: 34942.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The SME 244 and SME 275 in chain A are radiation induced modification of Methionine Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 34910.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-CL / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density meas: 622534.625 Mg/m3 / Density % sol: 44.71 % / Description: Three dimension rods |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium chloride 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.48→72.66 Å / Num. obs: 104530 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.48→1.62 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 24710 / CC1/2: 0.813 / Rpim(I) all: 0.253 / Rrim(I) all: 0.596 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5YU5 Resolution: 1.48→72.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.747 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.613 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→72.66 Å
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Refine LS restraints |
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