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- PDB-6qna: Structure of bovine anti-RSV hybrid Fab B13HC-B4LC -

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Basic information

Entry
Database: PDB / ID: 6qna
TitleStructure of bovine anti-RSV hybrid Fab B13HC-B4LC
Components
  • B13 Heavy chain
  • B4 light chain
KeywordsIMMUNE SYSTEM / cattle antibodies / bovine respiratory syncytial virus / anti-RSV B4 / anti-RSV B13 / hybrid Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsRen, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. ...Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. / Hammond, J. / Owens, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Mol.Immunol. / Year: 2019
Title: The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus.
Authors: Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. / Hammond, J. / Owens, R.J.
History
DepositionFeb 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: B13 Heavy chain
L: B4 light chain
A: B13 Heavy chain
B: B4 light chain
C: B13 Heavy chain
D: B4 light chain
E: B13 Heavy chain
F: B4 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,1489
Polymers194,0568
Non-polymers921
Water91951
1
H: B13 Heavy chain
L: B4 light chain


Theoretical massNumber of molelcules
Total (without water)48,5142
Polymers48,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-32 kcal/mol
Surface area20420 Å2
MethodPISA
2
A: B13 Heavy chain
B: B4 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6063
Polymers48,5142
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-34 kcal/mol
Surface area20520 Å2
MethodPISA
3
C: B13 Heavy chain
D: B4 light chain


Theoretical massNumber of molelcules
Total (without water)48,5142
Polymers48,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-33 kcal/mol
Surface area20020 Å2
MethodPISA
4
E: B13 Heavy chain
F: B4 light chain


Theoretical massNumber of molelcules
Total (without water)48,5142
Polymers48,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)43.440, 76.270, 130.030
Angle α, β, γ (deg.)89.66, 87.35, 88.60
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
B13 Heavy chain


Mass: 25837.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Homo sapiens (human)
#2: Antibody
B4 light chain


Mass: 22676.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28.0% w/v Polyethylene Glycol Monomethyl Ether 2000 0.1 M bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.62→65.9 Å / Num. obs: 49218 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shellResolution: 2.62→2.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.931 / Num. unique obs: 2446 / CC1/2: 0.521 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(dev_3386: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QN9
Resolution: 2.62→65.617 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.07
RfactorNum. reflection% reflection
Rfree0.2499 2230 4.53 %
Rwork0.2201 --
obs0.2214 49210 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→65.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13082 0 6 51 13139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213371
X-RAY DIFFRACTIONf_angle_d0.54718235
X-RAY DIFFRACTIONf_dihedral_angle_d14.2348008
X-RAY DIFFRACTIONf_chiral_restr0.0422148
X-RAY DIFFRACTIONf_plane_restr0.0042292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.6770.37581640.35462906X-RAY DIFFRACTION98
2.677-2.73930.41511710.33732886X-RAY DIFFRACTION98
2.7393-2.80780.34041490.3212922X-RAY DIFFRACTION98
2.8078-2.88370.33551510.30352956X-RAY DIFFRACTION98
2.8837-2.96860.34971270.29082901X-RAY DIFFRACTION98
2.9686-3.06440.34611320.2972976X-RAY DIFFRACTION98
3.0644-3.17390.33681290.28462952X-RAY DIFFRACTION98
3.1739-3.3010.26671170.27112991X-RAY DIFFRACTION99
3.301-3.45120.341180.27122917X-RAY DIFFRACTION98
3.4512-3.63310.29211300.25593005X-RAY DIFFRACTION98
3.6331-3.86070.29891030.25322916X-RAY DIFFRACTION98
3.8607-4.15880.26161270.21922949X-RAY DIFFRACTION99
4.1588-4.57720.20981630.17882936X-RAY DIFFRACTION99
4.5772-5.23930.18321640.16542917X-RAY DIFFRACTION98
5.2393-6.60.22661330.18812964X-RAY DIFFRACTION99
6.6-65.63740.19441520.17752886X-RAY DIFFRACTION97
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)
16.8321-2.6479-3.02814.58280.78864.8033-0.0103-0.38860.43550.01150.0717-0.50510.05940.28720.01310.456-0.0374-0.06430.47310.04260.600413.293480.711858.6054
25.9645-0.89570.98637.73130.42766.0330.4261-0.6496-0.33320.76140.0813-0.48870.3281-0.1824-0.38930.6716-0.0406-0.00420.67480.11430.7692-2.188968.368686.0207
35.42931.0614-1.60227.68360.36764.52540.05240.0602-0.4198-0.156-0.15070.010.72580.13930.01970.79840.14080.05070.42440.03360.666117.072559.939254.5628
44.81740.2939-4.98312.052-1.13198.6109-0.2121-0.0562-0.4694-0.15990.01020.21990.5971-0.53480.28590.3546-0.09-0.02950.5650.01220.65520.238662.12669.7938
53.15240.33331.449110.1015-0.71853.5776-0.058-0.278-0.3401-1.61460.49521.00920.2473-0.628-0.53230.9034-0.1676-0.02570.82350.21990.7897-12.459557.345778.52
65.950.4766-1.42535.52962.82155.0829-0.4756-1.1877-0.83160.850.30740.12461.2489-0.1199-0.03060.88990.02830.00780.77350.02560.5686-8.2355-16.2594-4.1478
73.9242-3.58281.89414.8776-0.15076.20370.14490.59820.1413-0.50590.1662-0.55050.02940.8074-0.03680.5431-0.0240.02350.712-0.12560.4813-5.8208-13.0729-14.583
81.9145-0.98941.16662.90651.15924.637-0.51061.3773-0.7730.62470.9596-0.61040.65570.5743-0.45040.6716-0.0069-0.0250.8807-0.16380.535-2.3571-17.481-8.1345
97.01570.2108-0.67798.35362.09024.67-0.1354-0.17620.5211-0.03870.04331.7585-0.4206-0.7650.08680.60960.04480.00810.6834-0.08110.9023-17.6321-5.4392-12.6711
102.39170.80021.96471.5028-0.71914.05530.5938-0.1627-0.23350.94640.0598-1.00970.25340.6684-0.46050.99810.2072-0.29851.3429-0.11290.6849.2227-4.81315.7287
113.83521.67222.44566.34190.13852.45530.5793-0.1292-0.18430.777-0.2308-0.14570.16040.3075-0.41760.95310.0852-0.10380.9888-0.02560.52355.0054-1.648319.2801
124.2970.3941-1.544.10641.9893.9380.4361-0.33760.25460.60410.5735-0.5237-0.27430.6483-0.71521.7781-0.0358-0.33451.40770.03650.75510.9928-3.456429.2942
135.9117-0.33541.98226.48890.79843.37290.11170.60730.615-0.67540.0163-0.0516-0.76820.1597-0.03521.2116-0.10810.08780.78140.16210.7889-7.960710.5923-16.943
145.41131.68990.95628.23571.16723.0848-0.2138-0.47121.5956-0.3106-0.12331.3562-0.822-0.6079-0.10850.7680.0934-0.06450.736-0.09231.1807-15.90795.0452-8.7346
155.9338-1.29972.4374.5467-0.6035.38670.55120.06951.0411-0.6147-0.22190.3703-1.2137-0.26880.00881.1070.04640.05450.70710.07861.0326-11.895511.0307-11.3742
163.9281-1.11221.45432.7444-2.63252.498-0.29970.00380.6277-1.26020.05920.2134-1.2385-0.14390.40890.753-0.04840.05840.83650.02580.7599-3.84799.1853-7.688
173.37411.74941.02064.37350.34813.36270.4193-1.6335-0.18640.25660.1712-0.81340.23360.2215-0.16790.90370.0876-0.12131.3769-0.05910.43916.3443.030418.5209
184.83561.76820.88763.224-0.49242.0608-0.08250.2538-1.1076-0.3797-0.0003-0.283-0.27460.8917-0.13491.18910.0201-0.02411.4483-0.13730.692213.527310.03447.6043
192.3738-0.40261.25624.4774-0.54112.3995-0.03430.4810.0019-0.60080.1024-1.3468-0.45661.8765-0.31461.0248-0.09820.04931.8873-0.33610.802220.6969.287915.3643
208.32013.8175-2.06557.9605-0.56453.8111-0.2307-0.35780.46040.05090.11630.6088-0.0465-0.4320.08920.38950.042-0.04440.5475-0.12510.5532-30.929341.5719-20.427
214.9952.1583-4.51610.0263-5.65055.86290.46190.8906-0.1176-0.0401-0.01750.7857-0.1242-0.1795-0.41460.5701-0.0878-0.01560.69890.00270.5959-15.816732.0791-47.5261
227.8408-0.0057-0.49334.27192.01685.5060.3963-0.4305-0.60560.4494-0.1777-0.27540.5738-0.2242-0.16820.7877-0.1274-0.01640.61890.13440.8068-35.002420.4443-18.5374
234.9232-0.3345-4.18783.85650.36364.87-0.4734-0.1596-0.6264-0.1862-0.1422-0.21980.67190.20950.470.5657-0.081-0.18060.65950.08440.6178-14.545422.1175-36.2361
244.4816-0.65710.60478.5597-1.02295.3120.008-0.0929-0.3333-0.1355-0.4222-1.96350.5730.54130.44720.9140.01150.07680.68930.10911.0992-4.295420.2549-42.9412
258.20763.08770.51732.7355-0.96035.6380.24880.05910.24940.18610.3087-0.32290.1015-0.1707-0.43990.75340.1165-0.03850.4648-0.03130.890828.480223.468447.5253
264.27950.21990.86763.93340.20274.2621-0.08930.41110.43010.53220.5138-1.2051-0.00610.4848-0.41740.73380.1351-00.5718-0.06951.318234.270930.971845.585
274.46511.20570.98274.2857-1.11743.48710.23460.57060.2855-0.6410.3450.1553-0.69290.5504-0.47291.0187-0.2121-0.09961.2939-0.03270.710714.618534.556719.0672
283.8742-1.2776-2.54942.06952.25353.66970.88010.26980.5435-1.2212-0.1997-0.0846-0.08890.232-0.60910.9559-0.1993-0.0921.3364-0.02960.804516.744631.94912.0871
294.7304-0.43511.79616.0838-2.07942.4554-0.06920.1388-0.39770.62730.4488-0.6658-0.55450.1027-0.39370.95360.12080.08490.5801-0.06551.214734.743446.319347.473
305.20151.99364.11434.7251.97784.1575-0.52030.2839-0.00970.22040.4517-0.5873-0.6879-0.02990.14660.70420.12410.25950.63780.00170.82324.936145.64737.9047
314.98231.02072.81777.34991.41516.1101-0.5561-0.21240.2199-0.1210.00880.7955-1.1238-0.76170.65561.04040.0181-0.05811.1383-0.01250.55795.94245.949223.265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 139 )
2X-RAY DIFFRACTION2chain 'H' and (resid 140 through 240 )
3X-RAY DIFFRACTION3chain 'L' and (resid 3 through 92 )
4X-RAY DIFFRACTION4chain 'L' and (resid 93 through 130 )
5X-RAY DIFFRACTION5chain 'L' and (resid 131 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2 through 33 )
7X-RAY DIFFRACTION7chain 'A' and (resid 34 through 72 )
8X-RAY DIFFRACTION8chain 'A' and (resid 73 through 90 )
9X-RAY DIFFRACTION9chain 'A' and (resid 91 through 126 )
10X-RAY DIFFRACTION10chain 'A' and (resid 127 through 174 )
11X-RAY DIFFRACTION11chain 'A' and (resid 175 through 223 )
12X-RAY DIFFRACTION12chain 'A' and (resid 224 through 238 )
13X-RAY DIFFRACTION13chain 'B' and (resid 3 through 33 )
14X-RAY DIFFRACTION14chain 'B' and (resid 34 through 62 )
15X-RAY DIFFRACTION15chain 'B' and (resid 63 through 92 )
16X-RAY DIFFRACTION16chain 'B' and (resid 93 through 115 )
17X-RAY DIFFRACTION17chain 'B' and (resid 116 through 141 )
18X-RAY DIFFRACTION18chain 'B' and (resid 142 through 173 )
19X-RAY DIFFRACTION19chain 'B' and (resid 174 through 213 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 139 )
21X-RAY DIFFRACTION21chain 'C' and (resid 140 through 235 )
22X-RAY DIFFRACTION22chain 'D' and (resid 3 through 92 )
23X-RAY DIFFRACTION23chain 'D' and (resid 93 through 152 )
24X-RAY DIFFRACTION24chain 'D' and (resid 153 through 213 )
25X-RAY DIFFRACTION25chain 'E' and (resid 2 through 90 )
26X-RAY DIFFRACTION26chain 'E' and (resid 91 through 139 )
27X-RAY DIFFRACTION27chain 'E' and (resid 140 through 197 )
28X-RAY DIFFRACTION28chain 'E' and (resid 198 through 236 )
29X-RAY DIFFRACTION29chain 'F' and (resid 3 through 62 )
30X-RAY DIFFRACTION30chain 'F' and (resid 63 through 130 )
31X-RAY DIFFRACTION31chain 'F' and (resid 131 through 213 )

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