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- PDB-4d53: Outer surface protein BB0689 from Borrelia burgdorferi -

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Basic information

Entry
Database: PDB / ID: 4d53
TitleOuter surface protein BB0689 from Borrelia burgdorferi
ComponentsBB0689
KeywordsSTRUCTURAL PROTEIN / LIPOPROTEIN / CAP DOMAIN / LYME DISEASE
Function / homologyPathogenesis-related Protein p14a / CAP / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein BB_0689
Function and homology information
Biological speciesBORRELIA BURGDORFERI (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsBrangulis, K. / Petrovskis, I. / Kazaks, A. / Tars, K.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and Functional Analysis of Bb0689 from Borrelia Burgdorferi, a Member of the Bacterial CAP Superfamily.
Authors: Brangulis, K. / Jaudzems, K. / Petrovskis, I. / Akopjana, I. / Kazaks, A. / Tars, K.
History
DepositionNov 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: BB0689
B: BB0689


Theoretical massNumber of molelcules
Total (without water)31,8332
Polymers31,8332
Non-polymers00
Water2,594144
1
A: BB0689


Theoretical massNumber of molelcules
Total (without water)15,9161
Polymers15,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BB0689


Theoretical massNumber of molelcules
Total (without water)15,9161
Polymers15,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.210, 92.210, 96.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein BB0689


Mass: 15916.275 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: O51632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.7 Å3/Da / Density % sol: 66.6 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 8.5

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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: Jun 27, 2013 / 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: 1.85→33.3 Å / Num. obs: 39106 / % possible obs: 99.1 % / Observed criterion σ(I): 2.1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 14.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.8 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.85→33.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.223 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21581 1966 5 %RANDOM
Rwork0.17824 ---
obs0.18015 37122 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 144 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022200
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9662944
X-RAY DIFFRACTIONr_angle_other_deg0.96935062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62924.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.815444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881516
X-RAY DIFFRACTIONr_chiral_restr0.1430.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02482
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_it2.772.5061062
X-RAY DIFFRACTIONr_mcbond_other2.7422.5011061
X-RAY DIFFRACTIONr_mcangle_it3.4663.7271324
X-RAY DIFFRACTIONr_mcangle_other3.4793.7321325
X-RAY DIFFRACTIONr_scbond_it4.7453.1111128
X-RAY DIFFRACTIONr_scbond_other4.7433.1151129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9284.4231621
X-RAY DIFFRACTIONr_long_range_B_refined8.45920.8242541
X-RAY DIFFRACTIONr_long_range_B_other8.4920.6492481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 123 -
Rwork0.242 2605 -
obs--95.12 %

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