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- PDB-7rpr: Borrelia miyamotoi FbpA complement inhibitory domain -

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Basic information

Entry
Database: PDB / ID: 7rpr
TitleBorrelia miyamotoi FbpA complement inhibitory domain
ComponentsFibronectin-binding lipoprotein FbpA
KeywordsIMMUNE SYSTEM / complement evasion / C1r / Borrelia
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Fibronectin-binding lipoprotein
Function and homology information
Biological speciesBorrelia miyamotoi FR64b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBooth, C.E. / Garcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146930 United States
CitationJournal: Front Immunol / Year: 2022
Title: Borrelia miyamotoi FbpA and FbpB Are Immunomodulatory Outer Surface Lipoproteins With Distinct Structures and Functions.
Authors: Booth Jr., C.E. / Powell-Pierce, A.D. / Skare, J.T. / Garcia, B.L.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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: Fibronectin-binding lipoprotein FbpA
B: Fibronectin-binding lipoprotein FbpA


Theoretical massNumber of molelcules
Total (without water)36,1772
Polymers36,1772
Non-polymers00
Water3,639202
1
A: Fibronectin-binding lipoprotein FbpA


Theoretical massNumber of molelcules
Total (without water)18,0881
Polymers18,0881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibronectin-binding lipoprotein FbpA


Theoretical massNumber of molelcules
Total (without water)18,0881
Polymers18,0881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.428, 40.320, 74.086
Angle α, β, γ (deg.)90.000, 105.407, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fibronectin-binding lipoprotein FbpA


Mass: 18088.406 Da / Num. of mol.: 2 / Fragment: FbpA complement inhibitory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia miyamotoi FR64b (bacteria) / Gene: BOM_1471, fbpA / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W5SFZ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion / Details: 12.8mg/mL, 0.1M tris (8.5), 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25861 / % possible obs: 97.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 23.74 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.068 / Rrim(I) all: 0.166 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2566 / CC1/2: 0.834 / Rpim(I) all: 0.276 / Rrim(I) all: 0.654

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N1L

6n1l


Resolution: 1.9→35.71 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.5846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 2000 7.74 %
Rwork0.2057 23840 -
obs0.2079 25840 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 202 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01352532
X-RAY DIFFRACTIONf_angle_d1.25053398
X-RAY DIFFRACTIONf_chiral_restr0.0594368
X-RAY DIFFRACTIONf_plane_restr0.007430
X-RAY DIFFRACTIONf_dihedral_angle_d19.2466986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.31051380.26981650X-RAY DIFFRACTION94.6
1.95-20.27041420.23381684X-RAY DIFFRACTION97.23
2-2.060.24751380.21181660X-RAY DIFFRACTION95.64
2.06-2.120.24091370.19181630X-RAY DIFFRACTION93.15
2.12-2.20.2331430.191696X-RAY DIFFRACTION97.56
2.2-2.290.22681450.19811730X-RAY DIFFRACTION99.47
2.29-2.390.25291450.20121726X-RAY DIFFRACTION99.26
2.39-2.520.2531460.20341741X-RAY DIFFRACTION99.26
2.52-2.680.25441420.21271708X-RAY DIFFRACTION98.14
2.68-2.880.26831430.21641698X-RAY DIFFRACTION96.89
2.88-3.170.2451380.21711647X-RAY DIFFRACTION93.9
3.17-3.630.23081480.19681758X-RAY DIFFRACTION98.81
3.63-4.570.17941460.19151745X-RAY DIFFRACTION98.59
4.58-35.710.22591490.21041767X-RAY DIFFRACTION96.18

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