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- PDB-6rjw: Crystal structure of the N-terminal domain of Lyme disease agent ... -

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Basic information

Entry
Database: PDB / ID: 6rjw
TitleCrystal structure of the N-terminal domain of Lyme disease agent Borrelia burgdorferi major virulence factor BB0323 (Se-Met data)
ComponentsLysM domain protein
KeywordsSTRUCTURAL PROTEIN / lipoprotein / spectrin repeats
Function / homology: / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / LysM domain protein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsBrangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structure of the N-terminal domain of the major virulence factor BB0323 from the Lyme disease agent Borrelia burgdorferi.
Authors: Brangulis, K. / Akopjana, I. / Kazaks, A. / Tars, K.
History
DepositionApr 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LysM domain protein


Theoretical massNumber of molelcules
Total (without water)22,4371
Polymers22,4371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.392, 48.829, 87.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LysM domain protein


Mass: 22436.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0323 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51302
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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KNO3 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97972 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2.85→43.9 Å / Num. obs: 4510 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 24
Reflection shellResolution: 2.85→3 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 15.6 / Num. unique obs: 636 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→43.9 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.862 / SU B: 14.919 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 205 4.6 %RANDOM
Rwork0.2051 ---
obs0.2079 4277 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.11 Å2 / Biso mean: 39.171 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.85→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 0 1360
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171312
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.6621841
X-RAY DIFFRACTIONr_angle_other_deg1.2631.5933055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9323.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7761510
X-RAY DIFFRACTIONr_chiral_restr0.070.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021519
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 15 -
Rwork0.259 314 -
all-329 -
obs--100 %

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