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- PDB-2yn7: Crystal structure of an outer surface protein BBA66 from Borrelia... -

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Basic information

Entry
Database: PDB / ID: 2yn7
TitleCrystal structure of an outer surface protein BBA66 from Borrelia burgdorferi
ComponentsOUTER SURFACE PROTEIN
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 / Outer surface protein
Function and homology information
Biological speciesBORRELIA BURGDORFERI B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / Ranka, R. / Baumanis, V. / Tars, K.
CitationJournal: Ticks Tick Borne Dis. / Year: 2014
Title: Crystal Structure of the Infectious Phenotype-Associated Outer Surface Protein Bba66 from the Lyme Disease Agent Borrelia Burgdorferi.
Authors: Brangulis, K. / Petrovskis, I. / Kazaks, A. / Tars, K. / Ranka, R.
History
DepositionOct 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: 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: OUTER SURFACE PROTEIN
B: OUTER SURFACE PROTEIN


Theoretical massNumber of molelcules
Total (without water)51,9792
Polymers51,9792
Non-polymers00
Water1,11762
1
A: OUTER SURFACE PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,9891
Polymers25,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OUTER SURFACE PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,9891
Polymers25,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.910, 51.120, 58.880
Angle α, β, γ (deg.)90.34, 96.21, 94.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein OUTER SURFACE PROTEIN


Mass: 25989.285 Da / Num. of mol.: 2 / Fragment: RESIDUES 191-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORRELIA BURGDORFERI B31 (bacteria) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50955
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.35 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 9 / Details: 18% PEG 2000 MME, 0.1 M TRIS PH 9.0

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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: Jul 1, 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: 2.24→33.01 Å / Num. obs: 21363 / % possible obs: 94.3 % / Observed criterion σ(I): 2.4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 85.2

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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: 2.25→29.78 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.255 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.226 / 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
Rfree0.23232 1076 5 %RANDOM
Rwork0.18805 ---
obs0.19032 20279 94.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.01 Å20.02 Å2
2---0.01 Å2-0.02 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 0 62 3552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9644732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33125.798188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19315711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6441518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022633
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: 2.248→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 78 -
Rwork0.298 1311 -
obs--83.37 %

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