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- PDB-4aly: Borrelia burgdorferi outer surface lipoprotein BBA64 -

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Basic information

Entry
Database: PDB / ID: 4aly
TitleBorrelia burgdorferi outer surface lipoprotein BBA64
ComponentsP35 ANTIGEN
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / OUTER SURFACE PROTEIN
Function / homology
Function and homology information


Bbcrasp-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
Similarity search - Domain/homology
P35 antigen / p35 antigen protein
Similarity search - Component
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsBrangulis, K. / Tars, K. / Petrovskis, I. / Kazaks, A. / Ranka, R. / Baumanis, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of an Outer Surface Lipoprotein Bba64 from the Lyme Disease Agent Borrelia Burgdorferi which is Critical to Ensure Infection After a Tick Bite
Authors: Brangulis, K. / Tars, K. / Petrovskis, I. / Kazaks, A. / Ranka, R. / Baumanis, V.
History
DepositionMar 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P35 ANTIGEN
B: P35 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9027
Polymers63,4222
Non-polymers4805
Water2,054114
1
A: P35 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9033
Polymers31,7111
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P35 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9994
Polymers31,7111
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.150, 70.140, 186.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, 0.02586, -0.1554), (0.001855, 0.937, 0.9276), (0.01182, 0.1315, -0.9361)
Vector: 0.7673, -0.1787, 0.3685)

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Components

#1: Protein P35 ANTIGEN / P35 ANTIGEN PROTEIN / BBA64


Mass: 31710.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI (Lyme disease spirochete)
Strain: B31 / Plasmid: PETM_11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70848, UniProt: H7C7P4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8
Details: 20% PEG 2000 MME 0.05 M (NH4)2SO4 15% GLYCEROL, pH 8.0

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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 9, 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: 2.4→40 Å / Num. obs: 25348 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→93.09 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.352 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26077 1292 5.1 %RANDOM
Rwork0.2135 ---
obs0.21588 24057 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→93.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 25 114 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.061.9684451
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21925.886175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17715629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3691517
X-RAY DIFFRACTIONr_chiral_restr0.1420.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022449
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 110 -
Rwork0.255 1602 -
obs--98.05 %

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