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Basic information

Entry
Database: PDB / ID: 6fl0
TitleCrystal structure of the membrane attack complex assembly inhibitor BGA71 from Lyme disease agent Borreliella bavariensis
Componentsmembrane attack complex assembly inhibitor BGA71
KeywordsIMMUNE SYSTEM / Outer surface protein / complement system inhibitor
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Complement regulator acquiring protein 1 / Uncharacterized protein
Function and homology information
Biological speciesBorreliella bavariensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBrangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
1.1.1.2/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 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
G: membrane attack complex assembly inhibitor BGA71
H: membrane attack complex assembly inhibitor BGA71
I: membrane attack complex assembly inhibitor BGA71
J: membrane attack complex assembly inhibitor BGA71
K: membrane attack complex assembly inhibitor BGA71
L: membrane attack complex assembly inhibitor BGA71
M: membrane attack complex assembly inhibitor BGA71
N: membrane attack complex assembly inhibitor BGA71
O: membrane attack complex assembly inhibitor BGA71
P: membrane attack complex assembly inhibitor BGA71
Q: membrane attack complex assembly inhibitor BGA71
R: membrane attack complex assembly inhibitor BGA71


Theoretical massNumber of molelcules
Total (without water)408,81018
Polymers408,81018
Non-polymers00
Water0
1
A: membrane attack complex assembly inhibitor BGA71
G: 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 area2080 Å2
ΔGint-16 kcal/mol
Surface area17790 Å2
MethodPISA
2
B: membrane attack complex assembly inhibitor BGA71

K: 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
crystal symmetry operation2_754-y+2,x-y,z-2/31
Buried area1940 Å2
ΔGint-15 kcal/mol
Surface area18070 Å2
MethodPISA
3
C: membrane attack complex assembly inhibitor BGA71

R: 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
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Buried area1970 Å2
ΔGint-15 kcal/mol
Surface area17830 Å2
MethodPISA
4
D: membrane attack complex assembly inhibitor BGA71

M: 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
crystal symmetry operation1_556x,y,z+11
Buried area2000 Å2
ΔGint-16 kcal/mol
Surface area17990 Å2
MethodPISA
5
E: membrane attack complex assembly inhibitor BGA71

Q: 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
crystal symmetry operation1_554x,y,z-11
Buried area2210 Å2
ΔGint-16 kcal/mol
Surface area17940 Å2
MethodPISA
6
F: membrane attack complex assembly inhibitor BGA71
O: 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 area2230 Å2
ΔGint-16 kcal/mol
Surface area17930 Å2
MethodPISA
7
H: membrane attack complex assembly inhibitor BGA71

L: 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
crystal symmetry operation1_554x,y,z-11
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area17940 Å2
MethodPISA
8
I: membrane attack complex assembly inhibitor BGA71
N: 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 area2100 Å2
ΔGint-17 kcal/mol
Surface area18070 Å2
MethodPISA
9
J: membrane attack complex assembly inhibitor BGA71
P: 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 area2190 Å2
ΔGint-15 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.176, 239.176, 56.253
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.: 18
Source method: isolated from a genetically manipulated source
Details: First four amino acids (GAMG) are remnants from the expression tag.
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: 2.27 Å3/Da / Density % sol: 45.87 %
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: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→119.59 Å / Num. obs: 79678 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.9
Reflection shellResolution: 2.9→2.96 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 9.7 / Num. unique obs: 4621 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Aimlessdata scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.9→59.87 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.883 / SU B: 15.412 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 4045 5.1 %RANDOM
Rwork0.1923 ---
obs0.1952 75682 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.42 Å2 / Biso mean: 32.086 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.9→59.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26099 0 0 0 26099
Num. residues----3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01426689
X-RAY DIFFRACTIONr_bond_other_d0.0010.01724687
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.6635842
X-RAY DIFFRACTIONr_angle_other_deg0.7791.64758100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68253154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91325.9121475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.095155555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7891572
X-RAY DIFFRACTIONr_chiral_restr0.0480.23686
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0229040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024504
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 300 -
Rwork0.195 5621 -
all-5921 -
obs--99.98 %

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