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- PDB-8b6a: Crystal structure of BfrB protein from Bacteroides fragilis NCTC 9343 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b6a | ||||||
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Title | Crystal structure of BfrB 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. / Conserved hypothetical lipoprotein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Antonyuk, S.V. / 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 | ![]() | 96 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b61C ![]() 6ewmS S: Starting model for refinement 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
#1: Protein | Mass: 23157.723 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_0985, NCTC9343_02639 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #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: 2.79 Å3/Da / Density % sol: 55 % / Description: plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.6M ammonium sulphate, 100mM sodium acetate, pH 5.5 |
-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: Mar 10, 2021 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→38.44 Å / Num. obs: 40527 / % possible obs: 96.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 13 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.141 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.458 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1756 / CC1/2: 0.346 / Rpim(I) all: 1.078 / % possible all: 75.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EWM Resolution: 1.77→38.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.945 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.139 / 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: 19.359 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→38.47 Å
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Refine LS restraints |
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