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- PDB-8b6a: Crystal structure of BfrB protein from Bacteroides fragilis NCTC 9343 -

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Basic information

Entry
Database: PDB / ID: 8b6a
TitleCrystal structure of BfrB protein from Bacteroides fragilis NCTC 9343
ComponentsConserved hypothetical lipoprotein
KeywordsUNKNOWN FUNCTION / HMUY like / heme binding
Function / homologyHmuY protein / HmuY protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAntonyuk, S.V. / Strange, R.W. / Olczak, T.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other government2019/33/B/NZ6/00292 Poland
CitationJournal: Faseb J. / Year: 2023
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
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical lipoprotein
B: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,16811
Polymers46,3152
Non-polymers8539
Water10,178565
1
A: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6306
Polymers23,1581
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5385
Polymers23,1581
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.465, 42.311, 110.392
Angle α, β, γ (deg.)90.00, 95.49, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Conserved hypothetical lipoprotein / Lipoprotein


Mass: 23157.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow
Gene: BF9343_0985, NCTC9343_02639 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LGH3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6M ammonium sulphate, 100mM sodium acetate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EWM

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
RfactorNum. reflection% reflectionSelection details
Rfree0.25913 2095 5.2 %RANDOM
Rwork0.2055 ---
obs0.2082 38371 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.359 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20.81 Å2
2---2.99 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.77→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 48 565 3285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132797
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152532
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.663813
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5815877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9275355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9423.884121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24415428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.788158
X-RAY DIFFRACTIONr_chiral_restr0.0570.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.8411408
X-RAY DIFFRACTIONr_mcbond_other1.11.841407
X-RAY DIFFRACTIONr_mcangle_it1.7472.7551758
X-RAY DIFFRACTIONr_mcangle_other1.7482.7561759
X-RAY DIFFRACTIONr_scbond_it1.7042.0561389
X-RAY DIFFRACTIONr_scbond_other1.6242.021369
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6082.9612022
X-RAY DIFFRACTIONr_long_range_B_refined4.97223.33256
X-RAY DIFFRACTIONr_long_range_B_other4.25122.2163093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 126 -
Rwork0.372 2175 -
obs--75.39 %

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