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- PDB-8b61: Crystal structure of BfrC protein from Bacteroides fragilis NCTC 9343 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b61 | ||||||
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Title | Crystal structure of BfrC protein from Bacteroides fragilis NCTC 9343 | ||||||
![]() | Conserved hypothetical lipoprotein | ||||||
![]() | UNKNOWN FUNCTION / HMUY like / heme binding | ||||||
Function / homology | HmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / pentane-1,3,5-tricarboxylic acid / Conserved hypothetical lipoprotein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antonyuk, S.V. / Barnett, K. / Strange, R.W. / Olczak, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bacteroides fragilis expresses three proteins similar to Porphyromonas gingivalis HmuY: Hemophore-like proteins differentially evolved to participate in heme acquisition in oral and gut microbiomes. Authors: Antonyuk, S.V. / Sieminska, K. / Smiga, M. / Strange, R.W. / Wagner, M. / Barnett, K.J. / Olczak, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302 KB | Display | ![]() |
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PDB format | ![]() | 241.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.7 KB | Display | ![]() |
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Full document | ![]() | 468.5 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b6aC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26682.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow Gene: BF9343_2078, NCTC9343_03740 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % / Description: needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02 M M Magnesium chloride hexahydrate, 0.1M HEPES at pH 7.5 and 22 % w/v Poly acrylic acid sodium salt 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2021 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→66.55 Å / Num. obs: 43116 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Biso Wilson estimate: 22.8 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.071 / Rrim(I) all: 0.178 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.421 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2286 / CC1/2: 0.372 / Rpim(I) all: 0.871 / Rrim(I) all: 1.8 / % possible all: 91.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: alpha fold Resolution: 1.81→66.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.518 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.14 / 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: 27.616 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→66.55 Å
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Refine LS restraints |
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