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- PDB-7uij: Structural studies of B5-OspC complex -

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Basic information

Entry
Database: PDB / ID: 7uij
TitleStructural studies of B5-OspC complex
Components
  • Monoclonal B5 Fab Heavy Chain
  • Monoclonal B5 Fab Light Chain
  • Outer surface protein C
KeywordsIMMUNE SYSTEM / Fab antibody / OspC Borrelia burgdorferi
Function / homologyexternal side of cell outer membrane / Lipoprotein, OspC-type / Outer surface protein C-like superfamily / Lipoprotein / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / membrane / Outer surface protein C
Function and homology information
Biological speciesMus musculus (house mouse)
Borreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N9301900040 United States
CitationJournal: Mbio / Year: 2023
Title: Structural Elucidation of a Protective B Cell Epitope on Outer Surface Protein C (OspC) of the Lyme Disease Spirochete, Borreliella burgdorferi.
Authors: Rudolph, M.J. / Davis, S.A. / Haque, H.M.E. / Weis, D.D. / Vance, D.J. / Piazza, C.L. / Ejemel, M. / Cavacini, L. / Wang, Y. / Mbow, M.L. / Gilmore, R.D. / Mantis, N.J.
History
DepositionMar 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Monoclonal B5 Fab Heavy Chain
L: Monoclonal B5 Fab Light Chain
A: Monoclonal B5 Fab Heavy Chain
B: Monoclonal B5 Fab Light Chain
C: Outer surface protein C
D: Outer surface protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8597
Polymers132,7976
Non-polymers621
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.729, 139.858, 205.669
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Monoclonal B5 Fab Heavy Chain


Mass: 25411.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Monoclonal B5 Fab Light Chain


Mass: 23458.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Outer surface protein C / PC


Mass: 17528.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: variant A / Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: ospC, BB_B19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07337
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM sodium cacodylate 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: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 44184 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 73.1 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.04 / Rrim(I) all: 0.093 / Χ2: 0.954 / Net I/σ(I): 6.8 / Num. measured all: 230675
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.755.11.44821770.4950.6981.6120.61999.6
2.75-2.85.11.1921630.5850.5741.3240.64499.9
2.8-2.855.11.02621700.6550.4951.1430.64299.7
2.85-2.915.10.81521770.7270.3930.9080.63699.6
2.91-2.975.20.65221540.8160.3120.7250.66999.7
2.97-3.045.10.51422170.8890.2460.5720.69499.7
3.04-3.125.20.40521490.9260.1940.450.71399.7
3.12-3.25.10.32321990.9410.1550.360.78399.5
3.2-3.350.23621340.9630.1150.2630.80499.4
3.3-3.44.40.19322250.9730.1010.2180.9299.5
3.4-3.524.90.14921690.9840.0740.1671.04199.7
3.52-3.665.80.13322130.9880.0610.1471.05599.6
3.66-3.835.80.10921970.9910.050.121.186100
3.83-4.035.70.08921990.9930.0410.0991.20499.7
4.03-4.295.60.07422170.9940.0350.0821.29899.6
4.29-4.625.30.0622270.9960.0290.0671.3899.5
4.62-5.085.30.05222250.9970.0250.0581.24599.5
5.08-5.815.30.04922470.9970.0240.0551.1799.6
5.81-7.324.70.04322830.9970.0220.0491.04899.5
7.32-505.50.03324420.9990.0160.0371.08999.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KI5, 3RKD, 1GGQ
Resolution: 2.701→49.469 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2123 4.81 %
Rwork0.204 41996 -
obs0.2065 44119 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 281.21 Å2 / Biso mean: 93.771 Å2 / Biso min: 35.21 Å2
Refinement stepCycle: final / Resolution: 2.701→49.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8825 0 4 32 8861
Biso mean--98.96 61.71 -
Num. residues----1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059011
X-RAY DIFFRACTIONf_angle_d0.78312218
X-RAY DIFFRACTIONf_chiral_restr0.0461395
X-RAY DIFFRACTIONf_plane_restr0.0041546
X-RAY DIFFRACTIONf_dihedral_angle_d3.5975400
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.701-2.76360.38751430.3269267097
2.7636-2.83270.36571260.30382777100
2.8327-2.90930.33071260.29612773100
2.9093-2.99490.31881580.27542729100
2.9949-3.09150.3121410.27142762100
3.0915-3.2020.28061540.2664277999
3.202-3.33020.29771470.264273899
3.3302-3.48170.2591370.23822801100
3.4817-3.66520.24281360.21942811100
3.6652-3.89470.2611530.20582771100
3.8947-4.19530.23871340.19572823100
4.1953-4.61720.23181430.1642813100
4.6172-5.28470.23371480.1664281599
5.2847-6.65560.25481330.20362896100
6.6556-49.4690.22781440.16533038100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6538-1.4028-0.70791.29710.29558.2766-0.12690.86990.2235-0.45810.55590.48211.00750.4297-0.40760.8969-0.19050.16410.5185-0.03390.6493-20.3967-36.68-105.6043
23.8379-0.2159-0.48751.1344-0.54853.27660.04470.307-0.45-0.3856-0.1653-0.11290.48580.22810.00660.7614-0.10550.06640.37240.00950.571-14.9516-33.5223-95.3771
35.31971.35253.97385.15751.9913.92970.3917-0.6336-1.16010.35490.01950.02531.1528-0.6595-0.42510.8058-0.16520.02070.56060.10260.6513-21.7191-40.3229-94.7234
42.65920.04961.45051.48460.8055.88140.215-0.04970.0205-0.1909-0.1985-0.00410.5388-0.3424-0.09040.5787-0.02430.11560.3904-0.06790.464-23.8471-30.0491-105.7961
57.3883-4.25185.52544.6736-5.67477.9377-0.25580.38541.6885-0.4175-0.10780.2273-1.4659-1.12360.84871.24320.1885-0.03780.9728-0.06661.0904-39.4259-13.9771-128.1433
64.1751-1.07522.34229.19072.80984.0970.27530.42790.409-1.1288-0.8936-0.5015-0.7036-0.35070.51810.91650.1079-0.02580.49620.07570.622-30.6566-20.0446-124.4835
74.1833-2.84482.99832.9825-3.91347.4914-0.0127-0.9910.1403-0.24180.45820.66360.5237-1.1119-0.40990.4602-0.18310.18530.7581-0.10470.7129-33.3196-15.013-87.5125
86.15740.01594.21183.93742.51526.46810.2056-0.7689-0.36810.5540.07380.03930.01160.4383-0.06860.4166-0.04750.14510.5087-0.02750.4858-23.8829-21.0465-84.4542
97.3884-1.03023.06935.5502-0.2934.0413-0.157-0.1950.38030.1054-0.0654-0.0153-0.1903-0.21010.23860.3327-0.03620.11920.4089-0.04820.479-22.5711-14.0458-90.3042
104.3712-4.44112.45884.9975-1.41022.08020.0013-0.10240.2571-0.1476-0.0473-0.2483-0.0075-0.33320.16310.4076-0.04870.07490.6722-0.04940.5769-27.8727-13.1455-95.0476
114.5609-4.41881.19626.5612-0.65194.2501-0.2636-0.6287-0.2434-0.00670.52760.30190.3916-0.5392-0.2850.6756-0.16620.2190.57680.00660.5439-23.1264-28.2777-85.3998
121.3390.4891.56572.61280.72892.90280.23240.5921-0.623-1.02-0.43951.16450.4302-0.53310.39140.86440.1159-0.37651.0321-0.36171.1453-41.7151-15.907-118.8671
132.4840.76111.94152.48511.78644.78690.49890.4435-1.2358-0.854-1.63141.735-0.5119-2.0503-0.18730.5029-0.0143-0.19521.1301-0.79441.4418-47.0273-14.0189-115.0594
142.4694-0.51550.80942.1260.05646.54171.01430.7508-0.53220.0816-0.7991.23241.8776-1.31380.08540.7817-0.0802-0.29651.0021-0.38181.3299-45.2733-19.95-117.9805
151.2741.0682.01757.47645.88822.02250.58680.4551-0.0978-2.2314-0.34671.96181.4839-0.38530.25030.820.2178-0.98482.0628-1.06432.0007-54.6204-19.1848-127.1257
162.10070.2926-2.2154.9249-0.79282.4635-0.45680.55610.4396-1.159-1.55262.84070.4483-1.46190.30260.85620.2548-0.42111.5208-0.44071.6661-52.5182-10.626-123.9055
179.3279-0.55275.73282.9728-2.39764.97870.1851-2.5458-0.1314-0.12490.276-0.39461.2047-0.9124-0.65150.8350.14580.16650.9296-0.01460.52918.2632-31.3479-40.8929
186.9811-1.786.79722.8388-2.65326.86510.0676-1.2982-0.55550.18830.29650.08340.4977-1.2113-0.35160.79390.01360.17160.74880.04680.5028.1167-31.1805-50.6163
193.5698-3.37373.08613.4959-2.40488.2519-0.20390.24850.17351.0167-0.0319-0.3315-0.40660.29990.39770.76890.05530.08650.6147-0.03070.41421.3378-25.3703-50.4666
205.42071.60472.31675.6962-0.6885.1768-0.02850.3993-0.6432-0.4765-0.0692-0.13410.86240.8521-0.15880.80020.07250.12110.7699-0.08830.554616.0987-33.1232-57.4655
215.4766-0.08593.43343.2637-1.38185.02130.32390.0024-0.5541-0.0331-0.0782-0.11650.65010.4241-0.13610.60360.07330.11240.5477-0.01640.373118.4096-30.8243-49.2425
225.6987-0.976-0.08049.2957-1.35391.3029-0.0049-0.29810.51732.1903-0.0642-0.4679-1.12970.25350.20951.4159-0.2442-0.07740.61430.08020.558329.515-15.8913-22.527
234.35281.73833.50615.6113-0.79013.4904-0.54990.13020.2282.027-0.73230.4172-1.43950.52590.54421.6306-0.20360.10130.51840.14090.644527.063-11.5331-26.1425
242.1216-1.3043-0.27429.46894.38842.2476-0.3228-1.13820.09471.3632-0.36851.6334-3.2424-0.10830.58672.8834-0.03320.08280.8675-0.12260.498723.9539-11.7861-14.6848
254.11531.08330.80715.13650.95566.7212-0.14080.47020.3220.05860.1125-0.2033-0.55860.2975-0.00190.4858-0.0920.040.53270.03510.495716.6783-8.9643-57.487
262.49221.04691.86242.91540.41294.7176-0.29330.01390.30470.5628-0.1813-0.1836-0.92340.83920.44770.7427-0.1622-0.0020.72420.09240.603625.2252-8.6048-42.0767
273.0494-1.05293.08698.9732-1.89285.28550.28081.03410.72840.8009-1.0252-1.605-0.77391.68871.06091.1219-0.3202-0.17961.05160.2580.917737.41-5.2352-32.2587
280.26260.0579-0.713.03531.70222.0725-0.42530.40040.42450.6909-0.4762-2.3243-0.82591.61830.89481.3384-0.6622-0.57431.37880.3971.529643.7966-4.836-26.219
297.6808-4.27630.46568.19690.62364.50790.36-0.9311-0.4052-0.4788-0.04110.20340.4776-0.0995-0.19840.3911-0.19060.08310.50540.03930.4225-5.2157-24.3603-75.1671
303.88080.9243.83354.4307-1.56616.7569-0.4749-1.16231.20930.43110.6144-0.9524-0.2868-0.1353-0.14170.3441-0.08490.1450.3695-0.01830.45621.1521-14.0052-75.882
316.0148-1.48132.11912.3158-0.41044.7380.030.27230.1576-1.29530.2821-1.57710.45610.7275-0.14390.506-0.01360.15170.5758-0.01570.58549.8284-20.0144-84.0612
322.21851.0886-0.57276.9720.13084.8723-0.16120.1828-0.2421-0.2326-0.0048-0.70190.79460.21350.02690.43110.0160.09780.4871-0.0450.4725-0.3363-24.5156-85.372
333.14272.8466-0.13988.7797-1.50852.37530.0896-0.1477-0.63050.1232-0.1951-0.52710.507-0.12640.17790.5455-0.01980.21390.6407-0.03660.5558-3.1286-29.8229-70.3994
344.178-1.28721.42196.79553.89854.11670.19340.10720.4701-0.3180.0709-1.8364-0.51692.234-0.76150.56740.0398-0.01250.66810.09570.8079.8708-4.6751-74.7477
356.85871.34991.2988.92510.91354.31140.4685-0.77630.17570.9309-0.22241.670.2454-0.6547-0.00610.4476-0.07350.14790.6514-0.06030.4047-11.1474-20.9559-68.9694
362.0073-0.38661.82151.4892-0.17144.4813-0.0626-0.825-0.23420.49520.29461.72570.5865-1.2974-0.05710.6008-0.22680.23611.11080.00870.869-16.2755-25.241-60.7725
372.3374-0.66271.94724.3966-0.76533.5893-0.4383-1.09440.40090.8498-0.2920.4504-0.8822-0.94420.50450.61980.10630.09251.0018-0.23940.6252-8.0937-8.6952-60.1487
385.2428-4.6996-2.57645.81556.42349.3237-1.0835-0.8862-0.73931.29231.89161.02971.5110.8881-0.780.854-0.15370.03830.98710.14090.6486-4.4597-38.021-61.4993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 40 )H18 - 40
3X-RAY DIFFRACTION3chain 'H' and (resid 41 through 91 )H41 - 91
4X-RAY DIFFRACTION4chain 'H' and (resid 92 through 127 )H92 - 127
5X-RAY DIFFRACTION5chain 'H' and (resid 128 through 148 )H128 - 148
6X-RAY DIFFRACTION6chain 'H' and (resid 149 through 215 )H149 - 215
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 25 )L1 - 25
8X-RAY DIFFRACTION8chain 'L' and (resid 26 through 38 )L26 - 38
9X-RAY DIFFRACTION9chain 'L' and (resid 39 through 75 )L39 - 75
10X-RAY DIFFRACTION10chain 'L' and (resid 76 through 90 )L76 - 90
11X-RAY DIFFRACTION11chain 'L' and (resid 91 through 101 )L91 - 101
12X-RAY DIFFRACTION12chain 'L' and (resid 102 through 132 )L102 - 132
13X-RAY DIFFRACTION13chain 'L' and (resid 133 through 150 )L133 - 150
14X-RAY DIFFRACTION14chain 'L' and (resid 151 through 186 )L151 - 186
15X-RAY DIFFRACTION15chain 'L' and (resid 187 through 197 )L187 - 197
16X-RAY DIFFRACTION16chain 'L' and (resid 198 through 214 )L198 - 214
17X-RAY DIFFRACTION17chain 'A' and (resid 1 through 17 )A1 - 17
18X-RAY DIFFRACTION18chain 'A' and (resid 18 through 32 )A18 - 32
19X-RAY DIFFRACTION19chain 'A' and (resid 33 through 44 )A33 - 44
20X-RAY DIFFRACTION20chain 'A' and (resid 45 through 60 )A45 - 60
21X-RAY DIFFRACTION21chain 'A' and (resid 61 through 114 )A61 - 114
22X-RAY DIFFRACTION22chain 'A' and (resid 115 through 157 )A115 - 157
23X-RAY DIFFRACTION23chain 'A' and (resid 158 through 187 )A158 - 187
24X-RAY DIFFRACTION24chain 'A' and (resid 188 through 215 )A188 - 215
25X-RAY DIFFRACTION25chain 'B' and (resid 1 through 75 )B1 - 75
26X-RAY DIFFRACTION26chain 'B' and (resid 76 through 128 )B76 - 128
27X-RAY DIFFRACTION27chain 'B' and (resid 129 through 172 )B129 - 172
28X-RAY DIFFRACTION28chain 'B' and (resid 173 through 208 )B173 - 208
29X-RAY DIFFRACTION29chain 'C' and (resid 46 through 89 )C46 - 89
30X-RAY DIFFRACTION30chain 'C' and (resid 90 through 114 )C90 - 114
31X-RAY DIFFRACTION31chain 'C' and (resid 115 through 145 )C115 - 145
32X-RAY DIFFRACTION32chain 'C' and (resid 146 through 200 )C146 - 200
33X-RAY DIFFRACTION33chain 'D' and (resid 43 through 82 )D43 - 82
34X-RAY DIFFRACTION34chain 'D' and (resid 83 through 89 )D83 - 89
35X-RAY DIFFRACTION35chain 'D' and (resid 90 through 120 )D90 - 120
36X-RAY DIFFRACTION36chain 'D' and (resid 121 through 140 )D121 - 140
37X-RAY DIFFRACTION37chain 'D' and (resid 141 through 169 )D141 - 169
38X-RAY DIFFRACTION38chain 'D' and (resid 170 through 200 )D170 - 200

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