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- PDB-8b61: Crystal structure of BfrC protein from Bacteroides fragilis NCTC 9343 -

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Basic information

Entry
Database: PDB / ID: 8b61
TitleCrystal structure of BfrC 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. / pentane-1,3,5-tricarboxylic acid / Lipoprotein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAntonyuk, S.V. / Barnett, K. / 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 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Experimental preparation / Category: citation / citation_author / exptl_crystal_grow
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 / _exptl_crystal_grow.temp
Revision 1.2May 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,0507
Polymers53,3652
Non-polymers6855
Water9,080504
1
A: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0714
Polymers26,6831
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Conserved hypothetical lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9793
Polymers26,6831
Non-polymers2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.075, 89.840, 99.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-590-

HOH

21B-605-

HOH

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Components

#1: Protein Conserved hypothetical lipoprotein / Lipoprotein


Mass: 26682.555 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_2078, NCTC9343_03740 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LDF1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-P7W / pentane-1,3,5-tricarboxylic acid


Mass: 204.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.58 Å3/Da / Density % sol: 52.35 % / Description: needles
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
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
RfactorNum. reflection% reflectionSelection details
Rfree0.25069 2219 5.2 %RANDOM
Rwork0.20122 ---
obs0.20378 40814 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2---0.12 Å2-0 Å2
3---0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.81→66.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 46 504 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152919
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6524544
X-RAY DIFFRACTIONr_angle_other_deg1.3641.5836716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24523.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81715483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8711516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
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_it1.2011.4171592
X-RAY DIFFRACTIONr_mcbond_other1.1931.4161591
X-RAY DIFFRACTIONr_mcangle_it2.0382.1091985
X-RAY DIFFRACTIONr_mcangle_other2.0372.111986
X-RAY DIFFRACTIONr_scbond_it1.5231.6641742
X-RAY DIFFRACTIONr_scbond_other1.5231.6651743
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3972.4172556
X-RAY DIFFRACTIONr_long_range_B_refined6.28828.57714681
X-RAY DIFFRACTIONr_long_range_B_other6.05727.17614183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.854 Å
RfactorNum. reflection% reflection
Rfree0.367 162 -
Rwork0.39 2732 -
obs--92.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0181.56680.54483.63391.65931.6109-0.09170.0375-0.07860.01910.1528-0.1730.01170.0849-0.0610.1180.01270.01160.0359-0.02690.026133.10841.769518.8845
22.13691.3591-0.44983.2847-0.62790.9024-0.0548-0.0423-0.0174-0.0778-0.02480.0150.10430.03930.07960.15250.0112-0.01690.01180.00440.013945.0621-28.49056.0022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 238
2X-RAY DIFFRACTION2B30 - 238

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