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- PDB-4b2f: N-terminal deletion mutant of an outer surface protein BBA73 from... -

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Basic information

Entry
Database: PDB / ID: 4b2f
TitleN-terminal deletion mutant of an outer surface protein BBA73 from Borrelia burgdorferi
ComponentsPUTATIVE ANTIGEN P35
KeywordsMEMBRANE 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: 1.88 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / 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
DepositionJul 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)24,9021
Polymers24,9021
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 74.340, 95.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PUTATIVE ANTIGEN P35 / BBA73


Mass: 24902.344 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DELETION MUTANT, RESIDUES 87-296
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: O50962
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.66 Å3/Da / Density % sol: 53.8 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES PH6.5, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0408
DetectorType: MARRESEARCH MAR 165 / Detector: CCD / Date: Jul 1, 2012 / Details: MULTILAYER MIRROR
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 1.88→24.2 Å / Num. obs: 21966 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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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 4AXZ

4axz


Resolution: 1.88→23.03 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.744 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23518 1120 5.1 %RANDOM
Rwork0.20453 ---
obs0.20606 20829 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.886 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 84 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.9542272
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.475203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84126.02388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.932157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021256
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: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 75 -
Rwork0.271 1355 -
obs--99.44 %

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