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- PDB-1rjl: Structure of the complex between OspB-CT and bactericidal Fab-H6831 -

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Basic information

Entry
Database: PDB / ID: 1rjl
TitleStructure of the complex between OspB-CT and bactericidal Fab-H6831
Components
  • (Outer surface protein B) x 2
  • Fab H6831 H-chain
  • Fab H6831 L-chain
KeywordsIMMUNE SYSTEM / Beta Sheet / Antibody-Protein Complex
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. / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich ...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. / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer surface protein B
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionNov 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 999SEQUENCE CHAINS A AND B: NO SUITABLE SEQUENCE DATABASE REFERENCE WAS FOUND AT THE TIME OF ...SEQUENCE CHAINS A AND B: NO SUITABLE SEQUENCE DATABASE REFERENCE WAS FOUND AT THE TIME OF PROCESSING. CHAIN C: THE SEQUENCE LISTED IN THE SEQRES FOR CHAIN C IS THE PORTION OF THE FOLLOWING CONSTRUCT THAT WAS CLEARLY OBSERVED IN THE DENSITY: ANKLDSKKLTRSNGTTLEYSQITDADNATKAVETLKNSIKLEGSLVVGKTTVEIK EGTVTLKREIEKDGKVKVFLNDTAGSNKKTGKWEDSTSTLTISADSKKTKDLVFL TDGTITVQQYNTAGTSLEGSASEIKNLSELKNALK THE AUTHORS DO NOT KNOW IF THE PORTION OF THE CONSTRUCT THAT WAS NOT OBSERVED IN THE DENSITY WAS MISSING DUE TO PROTEOLYSIS, OR WAS DISORDERED IN THE CRYSTAL. CHAIN D: THE AUTHORS SAW AN EXTRA BETA STRAND OF DENSITY THAT WAS NOT CONTINUOUS WITH THE MAIN BODY OF DENSITY (I.E. THERE WAS NO DENSITY FOR A CONNECTING LOOP) AND THAT DID NOT SHOW CLEAR SIDECHAIN DENSITY. THIS STRAND PRESUMABLY ARISES FROM SOME PORTION OR PORTIONS OF THE REMAINING 'UNOBSERVED' SEQUENCE ABOVE, BUT SINCE THE REGISTER WAS UNKNOWN, THE AUTHORS MODELLED IT AS A POLYALANINE STRAND, LISTED IN THE SEQRES AND COORDINATES AS UNK, UNKNOWN RESIDUE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab H6831 L-chain
B: Fab H6831 H-chain
C: Outer surface protein B
D: Outer surface protein B


Theoretical massNumber of molelcules
Total (without water)57,6324
Polymers57,6324
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.286, 37.271, 87.939
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-3-

UNK

21D-3-

UNK

DetailsThe biological assembly consists of one Fab:OspB-CT complex, which forms the asymmetric unit.

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Components

#1: Antibody Fab H6831 L-chain


Mass: 23218.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C
#2: Antibody Fab H6831 H-chain


Mass: 23659.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB-C
#3: Protein Outer surface protein B


Mass: 10310.563 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: OSPB, BBA16 / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS / References: UniProt: P17739
#4: Protein/peptide Outer surface protein B


Mass: 443.539 Da / Num. of mol.: 1 / Fragment: 5-residue polyunknown fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: OSPB, BBA16 / Plasmid: pET9c / Production host: Escherichia coli (E. coli) / Strain (production host): BL2(DE3)/pLysS
#5: Water ChemComp-HOH / water / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6553.56
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop5.6PEG3350, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop5.6PEG 3350, sodium citrate, isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2773vapor diffusion, hanging drop7.5PEG 3350, propionamide, MOPS, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98 Å
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30.09 Å / Num. obs: 17715 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 39.3 Å2 / Limit h max: 71 / Limit h min: -71 / Limit k max: 14 / Limit k min: -71 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 508735.16 / Observed criterion F min: 0.45 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.8 / % possible all: 87.6

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab portion of PDB ENTRY 1OSP

1osp


Resolution: 2.6→30.09 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1745 9.9 %Random
Rwork0.191 ---
obs-17715 92.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 35.2404 Å2 / ksol: 0.303959 e/Å3
Displacement parametersBiso max: 98.73 Å2 / Biso mean: 39.2 Å2 / Biso min: 1.43 Å2
Baniso -1Baniso -2Baniso -3
1--5.58 Å20 Å23 Å2
2--10.27 Å20 Å2
3----4.69 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→30.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 0 144 4188
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg27.2
X-RAY DIFFRACTIONx_torsion_impr_deg1.48
X-RAY DIFFRACTIONx_mcbond_it1.511.5
X-RAY DIFFRACTIONx_mcangle_it2.672
X-RAY DIFFRACTIONx_scbond_it1.982
X-RAY DIFFRACTIONx_scangle_it3.042.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.2432118.90.24518270.0172362203886.3
2.72-2.860.2531897.90.25518870.0182395207686.7
2.86-3.040.2312078.90.23118710.0162328207889.2
3.04-3.280.21424310.20.21320080.0142373225194.9
3.28-3.60.2032018.50.20120890.0142373229096.5
3.6-4.120.1792028.40.17821030.0132407230595.8
4.12-5.190.1432379.80.14220910.0092406232896.7
5.19-30.090.18125510.20.18220940.0112502234993.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramwater_rep.param
X-RAY DIFFRACTION2protein.topwater.top

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