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- PDB-7mzt: Borrelia burgdorferi BBK32-C in complex with an autolytic fragmen... -

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Basic information

Entry
Database: PDB / ID: 7mzt
TitleBorrelia burgdorferi BBK32-C in complex with an autolytic fragment of human C1r at 4.1A
Components
  • Complement C1r subcomponent heavy chain
  • Complement C1r subcomponent light chain
  • Fibronectin-binding protein BBK32
KeywordsPROTEIN BINDING / Lyme disease spirochete / Borrelia burgdorferi / complement system / classical pathway / protease inhibitor
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / fibronectin binding / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / molecular adaptor activity ...complement subcomponent C_overbar_1r_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / fibronectin binding / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / molecular adaptor activity / blood microparticle / immune response / innate immune response / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Coagulation Factor Xa inhibitory site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Prokaryotic membrane lipoprotein lipid attachment site profile. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Fibronectin-binding protein BBK32 / Complement C1r subcomponent
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.07 Å
AuthorsGarcia, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI146930 United States
CitationJournal: J Immunol. / Year: 2021
Title: A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes.
Authors: Garrigues, R.J. / Powell-Pierce, A.D. / Hammel, M. / Skare, J.T. / Garcia, B.L.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C1r subcomponent heavy chain
B: Complement C1r subcomponent light chain
I: Fibronectin-binding protein BBK32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4804
Polymers63,2593
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-17 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.619, 96.989, 108.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Complement C1r subcomponent heavy chain


Mass: 19210.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00736
#2: Protein Complement C1r subcomponent light chain


Mass: 27125.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00736
#3: Protein Fibronectin-binding protein BBK32


Mass: 16922.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: bbk32, BB_K32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50835
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.7 % / Description: Small plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium formate, 27.5% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.07→50 Å / Num. obs: 15139 / % possible obs: 85.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 92.77 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.164 / Net I/σ(I): 4.4
Reflection shellResolution: 4.07→4.25 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1455 / CC1/2: 0.903 / Rpim(I) all: 0.264

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qy0, 6n1l

2qy0

6n1l


Resolution: 4.07→44.26 Å / SU ML: 0.7545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.1386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Author states that there is a second copy of complex in the asymmetric unit, evidenced by the electron density and the unit cell diemnsions. But it could not be modeled due to density ...Details: Author states that there is a second copy of complex in the asymmetric unit, evidenced by the electron density and the unit cell diemnsions. But it could not be modeled due to density disordering and dataset anisotropicity.
RfactorNum. reflection% reflection
Rfree0.3725 850 10.08 %
Rwork0.369 7579 -
obs0.3693 8429 83.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 108.3 Å2
Refinement stepCycle: LAST / Resolution: 4.07→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 14 0 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794209
X-RAY DIFFRACTIONf_angle_d1.2875685
X-RAY DIFFRACTIONf_chiral_restr0.0636616
X-RAY DIFFRACTIONf_plane_restr0.0107729
X-RAY DIFFRACTIONf_dihedral_angle_d15.93361560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.07-4.320.3471170.34641086X-RAY DIFFRACTION73.35
4.32-4.660.36311350.32811198X-RAY DIFFRACTION81.18
4.66-5.130.36791350.36121222X-RAY DIFFRACTION82.09
5.13-5.860.37561420.37771286X-RAY DIFFRACTION86.02
5.87-7.380.39051610.40241377X-RAY DIFFRACTION91.28
7.39-44.260.37521600.37631410X-RAY DIFFRACTION88.15

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