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- PDB-6fmh: Crystal structure of the membrane attack complex assembly inhibit... -

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Basic information

Entry
Database: PDB / ID: 6fmh
TitleCrystal structure of the membrane attack complex assembly inhibitor BGA71 from Lyme disease agent Borreliella bavariensis (Native data)
Componentsmembrane attack complex assembly inhibitor BGA71
KeywordsIMMUNE SYSTEM / Outer surface protein / complement system inhibitor
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / Regulator / Uncharacterized protein
Function and homology information
Biological speciesBorreliella bavariensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBrangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
ERDF/CFCA/SEDA1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of the membrane attack complex assembly inhibitor BGA71 from the Lyme disease agent Borrelia bavariensis.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Kraiczy, P. / Tars, K.
History
DepositionJan 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: membrane attack complex assembly inhibitor BGA71
B: membrane attack complex assembly inhibitor BGA71
C: membrane attack complex assembly inhibitor BGA71
D: membrane attack complex assembly inhibitor BGA71
E: membrane attack complex assembly inhibitor BGA71
F: membrane attack complex assembly inhibitor BGA71


Theoretical massNumber of molelcules
Total (without water)136,2706
Polymers136,2706
Non-polymers00
Water00
1
A: membrane attack complex assembly inhibitor BGA71
B: membrane attack complex assembly inhibitor BGA71


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-14 kcal/mol
Surface area18200 Å2
MethodPISA
2
C: membrane attack complex assembly inhibitor BGA71
D: membrane attack complex assembly inhibitor BGA71


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area18270 Å2
MethodPISA
3
E: membrane attack complex assembly inhibitor BGA71
F: membrane attack complex assembly inhibitor BGA71


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-14 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.060, 137.060, 56.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
membrane attack complex assembly inhibitor BGA71


Mass: 22711.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella bavariensis (bacteria) / Gene: BGA71 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ASF4, UniProt: A0A7I6GVB3*PLUS

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 26% PEG 3350, 100 mM Tris, 200 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→68.53 Å / Num. obs: 28251 / % possible obs: 96.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3997 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FL0

6fl0


Resolution: 2.8→68.53 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 8.107 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.346
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1404 4.9 %RANDOM
Rwork0.1897 ---
obs0.191 27017 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 155.25 Å2 / Biso mean: 39.94 Å2 / Biso min: 4.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.8→68.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8400 0 0 0 8400
Num. residues----1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.5520.028498
X-RAY DIFFRACTIONr_bond_other_d0.0390.028320
X-RAY DIFFRACTIONr_angle_refined_deg2.7251.9711410
X-RAY DIFFRACTIONr_angle_other_deg2.794319199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42351006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12226.659440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.139151765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0851524
X-RAY DIFFRACTIONr_chiral_restr0.1580.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029510
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021848
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 128 -
Rwork0.144 1873 -
all-2001 -
obs--94.43 %

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