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- PDB-1p4p: Outer Surface Protein B of B. burgdorferi: crystal structure of t... -

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Basic information

Entry
Database: PDB / ID: 1p4p
TitleOuter Surface Protein B of B. burgdorferi: crystal structure of the C-terminal fragment
ComponentsOuter surface protein B
KeywordsMEMBRANE PROTEIN / INTERMOLECULAR BETA SHEET / EXTENDED BETA SHEET
Function / homology
Function and homology information


cell outer membrane / membrane
Similarity search - Function
Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Outer surface protein B
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBecker, M. / Bunikis, J. / Lade, B.D. / Dunn, J.J. / Barbour, A.G. / Lawson, C.L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Investigation of Borrelia burgdorferi OspB, a BactericidalFab Target.
Authors: Becker, M. / Bunikis, J. / Lade, B.D. / Dunn, J.J. / Barbour, A.G. / Lawson, C.L.
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer surface protein B


Theoretical massNumber of molelcules
Total (without water)15,6541
Polymers15,6541
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.800, 51.660, 158.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Outer surface protein B / OSPB


Mass: 15653.579 Da / Num. of mol.: 1 / Fragment: OspB C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: OSPB / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS / References: UniProt: P17739
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG550MME, Bicine, sodium bromide, sodium citrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979, 1.073
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: focusing mirror
RadiationMonochromator: two-crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.0731
ReflectionResolution: 2→50 Å / Num. all: 9012 / Num. obs: 8090 / % possible obs: 89.8 % / Observed criterion σ(F): -10 / Observed criterion σ(I): -10 / Redundancy: 23.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 34.1
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 12.6 / % possible all: 77.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSP

1osp


Resolution: 2→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used CNS for simulated annealing, followed by conjugate gradient minimization against the maximum likelihood function. Then ran Refmac, and followed with 1 step of B-factor refinement in CNS. ...Details: Used CNS for simulated annealing, followed by conjugate gradient minimization against the maximum likelihood function. Then ran Refmac, and followed with 1 step of B-factor refinement in CNS. The loop from residue 218 to residue 221 (LYS ASP GLY LYS) is poorly ordered (is not clearly defined in the density).
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 848 -RANDOM
Rwork0.2107 ---
all-7983 --
obs-7983 89 %-
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.19 Å20 Å20 Å2
2---10.8 Å20 Å2
3---5.63 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 0 118 1177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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