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- PDB-4axz: Borrelia burgdorferi outer surface lipoprotein BBA73 -

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Basic information

Entry
Database: PDB / ID: 4axz
TitleBorrelia burgdorferi outer surface lipoprotein BBA73
ComponentsPUTATIVE ANTIGEN P35
KeywordsMEMBRANE PROTEIN / LIPID BINDING PROTEIN / OUTER SURFACE LIPOPROTEIN
Function / homologyBbcrasp-1 / Bbcrasp-1 / Borrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / Orthogonal Bundle / Mainly Alpha / membrane / Antigen P35
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / Ranka, R. / Baumanis, V. / Tars, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Structural Characterization of the Borrelia Burgdorferi Outer Surface Protein Bba73 Implicates Dimerization as a Functional Mechanism.
Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Baumanis, V. / Tars, K.
History
DepositionJun 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE ANTIGEN P35


Theoretical massNumber of molelcules
Total (without water)31,7121
Polymers31,7121
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.630, 47.100, 34.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PUTATIVE ANTIGEN P35 / BBA73


Mass: 31712.143 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-296
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: O50962
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7 / Details: 0.1M HEPES, PH 7.0, 14% PEG 3350, 0.05M NAH2PO4

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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 19, 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: 2.08→40.13 Å / Num. obs: 15649 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 13.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ALY

4aly


Resolution: 2.09→40.15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.653 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.185 / 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
Rfree0.24472 781 5 %RANDOM
Rwork0.21355 ---
obs0.21513 14816 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.051 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 0 86 1881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9562443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57626.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7115373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.688157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021343
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: 2.088→2.142 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 51 -
Rwork0.231 961 -
obs--99.41 %

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