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- PDB-8tvd: Fab 221-11 in complex with OspA -

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Basic information

Entry
Database: PDB / ID: 8tvd
TitleFab 221-11 in complex with OspA
Components
  • Heavy chain of Fab 221-11
  • Light chain of Fab 221-11
  • Outer surface protein A
KeywordsIMMUNE SYSTEM/Membrane Protein / monoclonal antibody / IMMUNE SYSTEM / IMMUNE SYSTEM-Membrane Protein 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)
Borreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.077 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)75N93019C00040 United States
CitationJournal: To Be Published
Title: Fab 221-11 in complex with OspA
Authors: Rudolph, M.J. / Mantis, N.
History
DepositionAug 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of Fab 221-11
H: Heavy chain of Fab 221-11
E: Outer surface protein A
A: Light chain of Fab 221-11
B: Heavy chain of Fab 221-11
C: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,70413
Polymers147,0936
Non-polymers6127
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.812, 107.812, 316.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 2 molecules EC

#3: Protein Outer surface protein A


Mass: 26821.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: ospA / Production host: Escherichia coli B (bacteria) / References: UniProt: P0CL66

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody Light chain of Fab 221-11


Mass: 22921.387 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 Heavy chain of Fab 221-11


Mass: 23803.768 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)

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Non-polymers , 3 types, 18 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 4% pentaerythritol ethoxylate, 2.2 M ammonium sulfate, and 100 mM sodium acetate pH 4.6. 2.0 M Tri-ammonium citrate and 5% 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: Feb 14, 2021
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: 35457 / % possible obs: 99.4 % / Redundancy: 15.2 % / CC1/2: 0.6 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.05-3.116.12.96117190.5710.8530.7563.0580.318100
3.1-3.1614.92.44717580.5510.8430.6532.5340.321100
3.16-3.22162.26917390.6170.8730.582.3430.337100
3.22-3.2917.42.02517380.6610.8920.4952.0860.34399.9
3.29-3.3617.21.6817480.7890.9390.4131.7310.37499.9
3.36-3.4316.21.3817560.8020.9440.3511.4250.45199.9
3.43-3.5217.41.14717400.8810.9680.2811.1820.47299.9
3.52-3.6217.61.01517530.880.9670.2471.0460.478100
3.62-3.7217.30.86617530.9030.9740.2130.8930.579100
3.72-3.84170.71517600.9050.9750.1790.7380.6599.9
3.84-3.9816.40.61317650.9340.9830.1570.6340.76599.7
3.98-4.1415.70.52817550.9330.9820.1390.5470.89699.8
4.14-4.3314.50.43517630.9430.9850.1210.4531.22299.2
4.33-4.5612.20.35717530.9430.9850.1090.3741.62398.5
4.56-4.8411.60.32217660.8860.9690.1020.3391.81298.2
4.84-5.2113.10.30817570.9240.980.0920.3231.85198.8
5.21-5.7414.80.28817990.9610.990.0810.3011.87199
5.74-6.5715.50.25918200.9770.9940.0710.2691.86999.5
6.57-8.2712.80.20318590.9690.9920.0650.2152.32599.1
8.27-5010.30.12719560.9820.9960.0460.1362.9797.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.077→48.732 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1735 4.9 %
Rwork0.2343 --
obs0.2369 35384 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.077→48.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10053 0 31 11 10095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210270
X-RAY DIFFRACTIONf_angle_d0.58913903
X-RAY DIFFRACTIONf_dihedral_angle_d2.4986530
X-RAY DIFFRACTIONf_chiral_restr0.0441609
X-RAY DIFFRACTIONf_plane_restr0.0041741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.077-3.16720.39151300.35882666X-RAY DIFFRACTION95
3.1672-3.26940.37361370.33982759X-RAY DIFFRACTION100
3.2694-3.38620.34981540.30722759X-RAY DIFFRACTION100
3.3862-3.52170.34021490.27892771X-RAY DIFFRACTION100
3.5217-3.6820.2881250.24762795X-RAY DIFFRACTION100
3.682-3.8760.28371540.2432787X-RAY DIFFRACTION100
3.876-4.11880.28141460.23452807X-RAY DIFFRACTION100
4.1188-4.43660.27031390.20282790X-RAY DIFFRACTION99
4.4366-4.88270.26361380.1832798X-RAY DIFFRACTION98
4.8827-5.58830.23921420.19172820X-RAY DIFFRACTION99
5.5883-7.03730.32791670.24032868X-RAY DIFFRACTION99
7.0373-48.7320.24571540.21913029X-RAY DIFFRACTION98
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)
19.28592.7604-4.56964.0992-3.13583.58260.3543-1.95830.75591.1694-0.17240.0065-0.90390.374-0.32040.7665-0.04770.16440.9704-0.19020.51653.1236-28.0922-7.9133
23.9641-1.20560.77284.88570.88446.28210.9987-0.33470.7939-0.38740.07610.0899-0.97090.1774-1.00631.1227-0.04440.40371.1211-0.06810.5799-3.6845-24.9775-13.5374
32.1722.1865-1.21574.959-0.16280.7267-0.0140.218-0.0349-0.22530.2553-0.16660.23670.6396-0.12670.5133-0.0189-0.1340.96410.06450.3029-4.9499-46.797-12.9442
47.1794-2.193-1.04739.01296.37868.6987-0.0626-1.1952-0.87281.76050.9981-2.04191.0311.078-0.91830.60740.1278-0.25060.68440.0350.5383-5.9441-60.3297-2.9947
52.2955-1.93311.09716.52041.90232.44360.1375-0.169-0.2035-1.094-0.00790.1611-0.05120.2087-0.19250.5458-0.15140.03341.23140.0090.3752-5.8817-58.2587-8.6395
63.15031.65951.73377.22362.80212.43360.2868-0.1795-0.45640.6290.1268-0.27110.4324-0.2327-0.2460.9611-0.1187-0.05450.62670.07230.3493-8.9106-69.3843-8.2608
73.5096-2.77361.19427.9329-0.30343.87040.23640.40590.1478-0.4412-0.03810.3078-0.4437-0.1995-0.22430.6172-0.08110.15890.67350.1640.32414.1767-35.1893-32.869
82.4886-0.5296-1.95573.9456-5.14289.6021.0520.8151.1879-1.7914-0.7669-0.87750.08571.7612-0.34281.0282-0.08310.29691.13360.07810.873210.8652-25.7834-32.3533
90.80291.0218-0.01312.1204-0.8851.0650.2094-0.83960.4269-0.2254-0.2159-0.4227-0.4910.588-0.03460.8231-0.19720.28391.1453-0.09510.592612.9958-35.1901-34.7875
105.6953-3.76360.08193.0347-1.34873.21790.39530.08990.6367-0.2308-0.38050.6538-0.22350.43540.01870.4448-0.26240.19340.7350.0720.82913.8422-26.4315-26.0911
114.01282.35220.19573.51660.51640.5768-0.1430.4181-0.3586-0.73780.1631-0.3412-0.1413-0.5569-0.04410.5249-0.07-0.06731.2142-0.00890.3126-3.118-57.2803-25.5267
123.89220.6793-3.34722.24451.41514.7917-0.1337-0.75760.06840.16880.58670.1554-0.3633-0.0597-0.4830.60210.1047-0.04831.07140.14230.3895-4.3622-55.1918-23.117
130.0835-0.80510.30679.3212-0.88184.8490.03-0.10480.1879-0.47260.60691.87561.2452-1.0732-0.3930.6459-0.026-0.10811.35640.1250.2899-20.3185-58.5861-19.8393
147.03463.3192-0.54052.6873-0.29010.0516-0.58280.90470.0884-1.02820.2998-0.33280.003-0.95030.34350.6946-0.11120.03771.3938-0.01860.4425-10.9175-58.3335-30.9346
154.11961.255-2.24132.95672.45966.51621.252-1.06771.55530.801-0.96530.3384-0.0111-0.711-0.32141.1394-0.19510.73730.9396-0.10591.4711-8.8078-6.2898-15.1761
163.10080.4288-0.98572.3468-1.34880.9235-0.1291.4995-0.5925-0.4938-0.1089-0.69810.8222-0.48360.34821.4504-0.72481.34280.1114-0.18192.10310.89440.576-24.9523
175.03691.03710.73552.87221.14724.29680.0678-0.10040.1640.62740.01530.14260.68460.0462-0.24251.2820.12020.54770.5063-0.01061.05132.727611.2641-23.1237
185.7001-0.11952.46284.9760.66282.2641-0.5464-0.7398-0.04681.2120.47191.0284-0.0579-0.2581-0.1411.1515-0.2430.02541.2370.10390.327452.1755-26.3892-5.1241
191.85991.25051.80045.63841.56554.561-0.2718-0.66340.16310.38410.23851.28450.8355-0.92270.07060.8201-0.1980.18290.99020.15410.488648.7891-32.9706-11.3641
200.97170.1730.49650.80021.22532.16360.2887-0.1243-0.29560.0630.01050.0027-0.6072-0.20360.21491.2226-0.0969-0.18130.96760.0891-0.151257.26-25.7757-19.1952
219.11033.90922.03716.32830.52316.78880.3698-0.4275-0.43260.1063-0.18640.10050.6138-1.233-0.15581.0993-0.1994-0.10750.85820.17130.411357.3948-35.4925-12.1453
222.83231.77992.0953.26971.30882.65520.00220.04090.02980.0884-0.0839-0.0664-0.3398-0.4128-0.01871.2084-0.26780.02390.8475-0.07080.327955.1387-23.7061-10.9289
235.5603-2.23022.87845.7554-6.31988.2143-0.11740.38311.26460.5910.1571-0.6037-1.5407-0.45390.35521.82560.2825-0.33380.7794-0.10740.556863.10036.3727-13.873
242.1307-1.2199-0.13541.67420.7770.51210.6318-1.2281.52131.2735-0.83931.6444-0.7339-0.70110.3332.2473-0.03270.64710.9986-0.47061.613158.747513.4738-3.5553
257.4341-0.23442.06227.087-3.09414.6347-0.4774-1.23650.07770.4123-0.44760.32970.5142-0.00150.84690.8155-0.1159-0.09060.95340.00740.363560.141-4.6678-9.8072
268.2065-2.94271.1397.086-2.74913.1630.58960.93352.0653-0.8142-1.11050.0728-0.5815-0.57260.78191.98910.1796-0.13170.88090.0160.871357.199116.12-14.7718
270.76310.3145-0.8291.3945-2.53334.6383-0.0548-0.12840.14581.49070.4586-0.4985-0.59820.2569-0.3072.2971-0.0756-0.25270.9258-0.12710.857665.924911.6151-4.3004
283.78170.99390.78315.4860.0834.1967-0.50650.22560.3096-0.60440.32720.41490.1166-0.27580.23940.8244-0.1549-0.10930.5376-0.02470.286646.1957-23.7604-32.5222
292.03520.38370.91882.58271.20641.9992-0.16820.21470.2426-0.81880.06740.35380.013-0.73680.10350.8155-0.0088-0.050.93280.11450.360844.0489-21.1592-30.4244
309.31121.3940.12042.5389-0.3680.4335-0.22110.70060.34480.32460.2061-0.2338-0.16110.52410.05850.88540.0476-0.11070.76360.05270.425263.19330.6316-24.2336
312.7252.1442-3.75366.545-0.29237.06250.0657-0.904-1.06710.10770.3415-1.50.65270.3628-0.61860.60520.0372-0.21720.97980.16851.347367.5468-58.4488-10.096
328.10771.89422.92353.8169-4.16798.00970.542-0.50891.0111-0.1782-0.5311-0.75790.63881.34590.06361.3466-0.38790.27041.325-0.29141.127967.666-53.2024-15.2973
339.0008-1.28591.3614.8445-6.03139.62090.1518-0.076-0.6046-0.04240.3443-0.25060.3670.5018-0.4530.7803-0.2409-0.00660.5473-0.19570.548657.1345-51.3722-19.1121
346.75814.51161.49277.31641.02973.91010.09040.6474-0.63960.1485-0.18440.039-0.78390.75620.12770.5778-0.0982-0.1380.47730.040.813534.0605-57.9961-29.3508
359.39-0.40652.88018.5206-3.6925.466-0.3740.0862-1.42420.79490.10720.0047-0.0202-0.6870.32180.74270.08040.2110.5856-0.01790.826818.2563-72.7409-24.8607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain 'L' and (resid 39 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 139 )
4X-RAY DIFFRACTION4chain 'L' and (resid 140 through 150 )
5X-RAY DIFFRACTION5chain 'L' and (resid 151 through 172 )
6X-RAY DIFFRACTION6chain 'L' and (resid 173 through 212 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 44 )
8X-RAY DIFFRACTION8chain 'H' and (resid 45 through 60 )
9X-RAY DIFFRACTION9chain 'H' and (resid 61 through 91 )
10X-RAY DIFFRACTION10chain 'H' and (resid 92 through 111 )
11X-RAY DIFFRACTION11chain 'H' and (resid 112 through 151 )
12X-RAY DIFFRACTION12chain 'H' and (resid 152 through 185 )
13X-RAY DIFFRACTION13chain 'H' and (resid 186 through 199 )
14X-RAY DIFFRACTION14chain 'H' and (resid 200 through 220 )
15X-RAY DIFFRACTION15chain 'E' and (resid 34 through 110 )
16X-RAY DIFFRACTION16chain 'E' and (resid 111 through 168 )
17X-RAY DIFFRACTION17chain 'E' and (resid 169 through 272 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1 through 18 )
19X-RAY DIFFRACTION19chain 'A' and (resid 19 through 38 )
20X-RAY DIFFRACTION20chain 'A' and (resid 39 through 49 )
21X-RAY DIFFRACTION21chain 'A' and (resid 50 through 75 )
22X-RAY DIFFRACTION22chain 'A' and (resid 76 through 113 )
23X-RAY DIFFRACTION23chain 'A' and (resid 114 through 143 )
24X-RAY DIFFRACTION24chain 'A' and (resid 144 through 155 )
25X-RAY DIFFRACTION25chain 'A' and (resid 156 through 174 )
26X-RAY DIFFRACTION26chain 'A' and (resid 175 through 188 )
27X-RAY DIFFRACTION27chain 'A' and (resid 189 through 212 )
28X-RAY DIFFRACTION28chain 'B' and (resid 1 through 60 )
29X-RAY DIFFRACTION29chain 'B' and (resid 61 through 127 )
30X-RAY DIFFRACTION30chain 'B' and (resid 128 through 220 )
31X-RAY DIFFRACTION31chain 'C' and (resid 24 through 48 )
32X-RAY DIFFRACTION32chain 'C' and (resid 49 through 66 )
33X-RAY DIFFRACTION33chain 'C' and (resid 67 through 121 )
34X-RAY DIFFRACTION34chain 'C' and (resid 122 through 203 )
35X-RAY DIFFRACTION35chain 'C' and (resid 204 through 272 )

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