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- PDB-4bg5: Lyme disease associated outer surface protein BBA65 from Borrelia... -

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Basic information

Entry
Database: PDB / ID: 4bg5
TitleLyme disease associated outer surface protein BBA65 from Borrelia burgdorferi
ComponentsBBA65
KeywordsMEMBRANE PROTEIN
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha / Lipoprotein, putative
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / Tars, K.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural analysis of the outer surface proteins from Borrelia burgdorferi paralogous gene family 54 that are thought to be the key players in the pathogenesis of Lyme disease
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
History
DepositionMar 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 22, 2020Group: Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: BBA65
B: BBA65


Theoretical massNumber of molelcules
Total (without water)60,3352
Polymers60,3352
Non-polymers00
Water00
1
A: BBA65


Theoretical massNumber of molelcules
Total (without water)30,1671
Polymers30,1671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BBA65


Theoretical massNumber of molelcules
Total (without water)30,1671
Polymers30,1671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.810, 69.870, 58.880
Angle α, β, γ (deg.)90.00, 101.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BBA65 / LIPOPROTEIN / PUTATIVE


Mass: 30167.396 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: B31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50954

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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: 2.46 Å3/Da / Density % sol: 50.1 % / Description: NONE
Crystal growpH: 6.5 / Details: 29% PEG 2000, 0.1M MES PH 6.5, 0.3M IMIDAZOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2012 / Details: RH-COATED TOROIDAL SI MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.68 Å / Num. obs: 7294 / % possible obs: 91.6 % / Observed criterion σ(I): 1.6 / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.5
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AXZ

4axz


Resolution: 3.4→48.79 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.849 / SU B: 18.758 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22927 346 4.7 %RANDOM
Rwork0.16478 ---
obs0.16794 6946 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.889 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å21.1 Å2
2--1.64 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 0 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023311
X-RAY DIFFRACTIONr_bond_other_d0.0010.023306
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9824446
X-RAY DIFFRACTIONr_angle_other_deg0.76437644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73526.447152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.90715698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.559158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5322.9881596
X-RAY DIFFRACTIONr_mcbond_other1.5312.9891595
X-RAY DIFFRACTIONr_mcangle_it2.6544.4761988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5343.1991715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 16 -
Rwork0.171 534 -
obs--97 %

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