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- PDB-7jwg: OspA-Fab 221-7 complex structure -

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Basic information

Entry
Database: PDB / ID: 7jwg
TitleOspA-Fab 221-7 complex structure
Components
  • Antibody 221-7 Fab heavy chain
  • Antibody 221-7 Fab light chain
  • Outer surface protein A
KeywordsIMMUNE SYSTEM / OspA-Fab complex
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein A
Function and homology information
Biological speciesHomo sapiens (human)
Borrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsRudolph, M.J.
CitationJournal: J.Clin.Invest. / Year: 2021
Title: Blocking Borrelia burgdorferi transmission from infected ticks to nonhuman primates with a human monoclonal antibody.
Authors: Schiller, Z.A. / Rudolph, M.J. / Toomey, J.R. / Ejemel, M. / LaRochelle, A. / Davis, S.A. / Lambert, H.S. / Kern, A. / Tardo, A.C. / Souders, C.A. / Peterson, E. / Cannon, R.D. / Ganesa, C. ...Authors: Schiller, Z.A. / Rudolph, M.J. / Toomey, J.R. / Ejemel, M. / LaRochelle, A. / Davis, S.A. / Lambert, H.S. / Kern, A. / Tardo, A.C. / Souders, C.A. / Peterson, E. / Cannon, R.D. / Ganesa, C. / Fazio, F. / Mantis, N.J. / Cavacini, L.A. / Sullivan-Bolyai, J. / Hu, L.T. / Embers, M.E. / Klempner, M.S. / Wang, Y.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody 221-7 Fab heavy chain
L: Antibody 221-7 Fab light chain
C: Outer surface protein A
A: Antibody 221-7 Fab heavy chain
B: Antibody 221-7 Fab light chain
E: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)146,5606
Polymers146,5606
Non-polymers00
Water23413
1
H: Antibody 221-7 Fab heavy chain
L: Antibody 221-7 Fab light chain
C: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)73,2803
Polymers73,2803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Antibody 221-7 Fab heavy chain
B: Antibody 221-7 Fab light chain
E: Outer surface protein A


Theoretical massNumber of molelcules
Total (without water)73,2803
Polymers73,2803
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.383, 99.263, 121.616
Angle α, β, γ (deg.)90.000, 103.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Antibody 221-7 Fab heavy chain


Mass: 23846.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Antibody 221-7 Fab light chain


Mass: 22395.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Outer surface protein A


Mass: 27037.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospA, BB_A15 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL66
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM NaCacodylate pH 6.5, 5% PEG 8K, and 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 38023 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 71.65 Å2 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.099 / Rrim(I) all: 0.193 / Χ2: 0.712 / Net I/σ(I): 3.7 / Num. measured all: 143795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.13.82.00218900.5351.1822.3260.56298.6
3.1-3.163.81.71918590.5651.0161.9980.5898.7
3.16-3.223.81.37919040.6430.8161.6040.59498.9
3.22-3.293.81.07918880.7340.6391.2550.58599
3.29-3.363.80.90618590.760.5371.0550.62198.8
3.36-3.433.80.6519290.8810.3850.7560.61599
3.43-3.523.80.5718680.90.3380.6630.64198.9
3.52-3.623.80.46618690.9470.2760.5420.67299
3.62-3.723.80.41918840.8880.2480.4870.98999.1
3.72-3.843.80.38419120.9580.2270.4470.66799.2
3.84-3.983.80.31819000.9640.1890.370.71299.2
3.98-4.143.80.23919180.980.1420.2780.66499.3
4.14-4.333.80.16818950.9880.10.1960.6999.2
4.33-4.563.80.11718750.9940.070.1370.72899.4
4.56-4.843.80.10319000.9950.0620.1210.799.4
4.84-5.213.70.09919280.9940.0590.1150.73799.5
5.21-5.743.70.119040.9930.060.1170.73999.5
5.74-6.573.60.10519200.9910.0640.1240.79999.5
6.57-8.273.70.06419600.9970.0380.0750.82199.7
8.27-503.70.0319610.9990.0180.0351.13199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HWB

4hwb


Resolution: 3.05→48.906 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 37.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3056 1900 5.01 %
Rwork0.2687 36059 -
obs0.2705 37959 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.8 Å2 / Biso mean: 95.2225 Å2 / Biso min: 22.61 Å2
Refinement stepCycle: final / Resolution: 3.05→48.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10217 0 0 13 10230
Biso mean---49.23 -
Num. residues----1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310393
X-RAY DIFFRACTIONf_angle_d0.88114056
X-RAY DIFFRACTIONf_chiral_restr0.0541638
X-RAY DIFFRACTIONf_plane_restr0.0051763
X-RAY DIFFRACTIONf_dihedral_angle_d3.8566285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.05-3.1260.43521330.424249795
3.126-3.21050.38311190.3968255199
3.2105-3.3050.44911140.3785257199
3.305-3.41160.38371280.3533255799
3.4116-3.53350.41611260.3354256999
3.5335-3.6750.40611350.3297257599
3.675-3.84220.39521380.3075257099
3.8422-4.04460.35211240.2878256799
4.0446-4.29790.27541300.2633257099
4.2979-4.62950.2471760.2297256099
4.6295-5.0950.24151550.2178257899
5.095-5.83120.25631440.2234260599
5.8312-7.34270.2941440.252606100
7.3427-48.9060.24981340.2065268399

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