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- PDB-6tco: Crystal structure of the omalizumab Fab Leu158Pro light chain mut... -

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Basic information

Entry
Database: PDB / ID: 6tco
TitleCrystal structure of the omalizumab Fab Leu158Pro light chain mutant - crystal form I
Components(Omalizumab Fab Leu158Pro light chain mutant) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / immunoglobulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMitropoulou, A.N. / Ceska, T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
Wellcome Trust085944 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Engineering the Fab fragment of the anti-IgE omalizumab to prevent Fab crystallization and permit IgE-Fc complex crystallization.
Authors: Mitropoulou, A.N. / Ceska, T. / Heads, J.T. / Beavil, A.J. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J. / Davies, A.M.
History
DepositionNov 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Omalizumab Fab Leu158Pro light chain mutant
H: Omalizumab Fab Leu158Pro light chain mutant
A: Omalizumab Fab Leu158Pro light chain mutant
B: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,85128
Polymers97,1574
Non-polymers1,69424
Water8,971498
1
L: Omalizumab Fab Leu158Pro light chain mutant
H: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,52215
Polymers48,5792
Non-polymers94313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-58 kcal/mol
Surface area18650 Å2
MethodPISA
2
A: Omalizumab Fab Leu158Pro light chain mutant
B: Omalizumab Fab Leu158Pro light chain mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,32913
Polymers48,5792
Non-polymers75111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-32 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.465, 116.844, 181.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-407-

HOH

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Components

#1: Antibody Omalizumab Fab Leu158Pro light chain mutant


Mass: 23906.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Omalizumab Fab Leu158Pro light chain mutant / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody Omalizumab Fab Leu158Pro light chain mutant


Mass: 24672.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Omalizumab Fab heavy chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350 and 0.2M sodium sulphate. Crystals were cryoprotected with 20% PEG 3350, 0.2M magnesium sulphate and 18% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.8→47.232 Å / Num. obs: 92713 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.031 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.572 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4559 / CC1/2: 0.596 / Rpim(I) all: 0.513 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TCM

6tcm


Resolution: 1.8→47.232 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 19.43
RfactorNum. reflection% reflection
Rfree0.1922 4613 4.98 %
Rwork0.1676 --
obs0.1688 92661 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.99 Å2 / Biso mean: 33.3157 Å2 / Biso min: 14.79 Å2
Refinement stepCycle: final / Resolution: 1.8→47.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 102 498 7063
Biso mean--56.02 38.84 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116852
X-RAY DIFFRACTIONf_angle_d1.1489381
X-RAY DIFFRACTIONf_chiral_restr0.0751052
X-RAY DIFFRACTIONf_plane_restr0.0071199
X-RAY DIFFRACTIONf_dihedral_angle_d14.1464082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.82050.33331400.30982905
1.8205-1.84190.30021420.27212922
1.8419-1.86440.30491520.25872891
1.8644-1.8880.27921610.24162949
1.888-1.91280.25911650.22052868
1.9128-1.9390.22061600.19982900
1.939-1.96670.21661500.19122926
1.9667-1.99610.22581500.18672885
1.9961-2.02730.23151590.19392899
2.0273-2.06050.22031500.1842901
2.0605-2.0960.18841700.17972907
2.096-2.13410.21361400.17852941
2.1341-2.17520.21251490.17642898
2.1752-2.21960.19221240.17022959
2.2196-2.26780.20491350.17362946
2.2678-2.32060.19921670.17092888
2.3206-2.37860.19771550.17042919
2.3786-2.44290.21661400.17422959
2.4429-2.51480.21991580.1842943
2.5148-2.5960.22921610.17762910
2.596-2.68880.19991530.17642948
2.6888-2.79640.18961410.18192946
2.7964-2.92370.19941800.18212905
2.9237-3.07780.20771800.17882912
3.0778-3.27060.2191840.18252941
3.2706-3.5230.2141610.16462927
3.523-3.87740.15091520.15772970
3.8774-4.43810.13621330.12513035
4.4381-5.59010.1221520.11942998
5.5901-47.2320.18131490.15743150
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23850.2436-0.24510.4798-0.39690.17260.21150.52830.0958-0.3449-0.1457-0.0688-0.0056-0.03240.00760.26370.0180.01710.3487-0.05580.244929.36072.05989.1923
20.8596-0.23070.41390.529-0.52590.7936-0.00380.1672-0.26720.02520.07170.01040.09630.00580.570.21790.0377-0.03360.257-0.11690.237229.1903-8.466514.5029
30.33070.2370.11230.17510.02710.3709-0.04270.2072-0.0567-0.05010.0558-0.04330.01980.00820.0010.19930.0335-0.02570.2578-0.06050.201228.46992.570716.5047
40.67080.2113-0.42570.2671-0.08371.1018-0.0095-0.00210.21690.54160.14930.2123-0.6546-0.25340.21640.4504-0.0218-0.07530.1038-0.05790.172629.853932.355139.2969
50.1885-0.16640.06740.1832-0.07580.31920.04620.23460.07630.06170.0854-0.1387-0.08270.0790.0020.2614-0.0237-0.02220.24540.01550.254726.842828.235125.364
60.3883-0.00180.3280.0474-0.12920.63630.09010.10560.1381-0.0107-0.14840.045-0.05880.070800.24340.0001-0.0260.2499-0.00550.274327.705624.378224.9812
70.293-0.07-0.00670.7919-0.36860.5407-0.08570.06890.3114-0.12930.0377-0.0588-0.41790.03260.04830.3694-0.0257-0.08790.21580.02070.368828.210236.547729.1597
80.02190.057-0.21370.21740.09610.15110.0639-0.0708-0.05780.2827-0.0305-0.21850.0639-0.0059-00.32920.0161-0.10930.2901-0.07780.361242.1124-7.271336.1571
90.90160.1573-0.04850.27550.27930.7078-0.09640.0778-0.11420.00270.027-0.483-0.01380.07310.00520.21140.0387-0.05690.2171-0.0820.422446.5046-9.159527.41
100.02670.0263-0.09580.17140.220.1235-0.1112-0.0498-0.2711-0.08790.0247-0.68530.17120.111300.30940.0356-0.11560.3247-0.09810.497249.9601-2.909532.3084
110.0029-0.01770.05840.18310.02310.07890.02340.0036-0.07270.1561-0.0775-0.0820.11650.0393-0.08940.26620.03-0.06890.2424-0.09580.31639.7214-3.698129.2742
120.01170.01140.02080.1192-0.03750.04920.04220.17760.46610.1843-0.0162-0.0315-0.1989-0.1482-0.00010.280.03760.00090.29380.00930.25128.687825.079739.9285
130.905-0.03810.8860.7148-0.36570.97770.10580.0026-0.07130.15810.0596-0.0424-0.0109-0.17690.010.23350.0018-0.03170.28620.03970.217328.869818.380640.4672
141.0213-0.32670.12981.68570.92160.4706-0.0583-0.17440.06940.1470.01770.03440.0166-0.036-0.02530.22490.0131-0.00210.2315-0.02590.158387.076916.216329.991
151.1761-0.8655-0.05150.79440.50811.907-0.1771-0.35190.03380.2503-0.00910.2001-0.0306-0.4641-0.01690.23850.02370.03120.3788-0.06640.366453.711223.854216.0115
160.6340.4987-0.0180.82160.18960.6421-0.0262-0.0258-0.1375-0.0583-0.02670.08980.09460.019-00.21-0.0097-0.01310.1799-0.00530.169989.3328-0.869313.7683
170.2307-0.17940.11310.1149-0.24480.0532-0.0825-0.164-0.3053-0.08860.0340.17160.11220.1419-0.00010.2527-0.0291-0.00650.244-0.01370.275382.622-5.074913.1288
180.38240.13610.20570.01450.16080.39890.0466-0.0201-0.03440.008-0.04510.04090.0245-0.012400.1875-0.0064-0.01790.1813-0.02140.207580.25147.866912.9012
190.9103-0.2758-0.00521.37121.35020.98870.10510.02260.1122-0.1542-0.0698-0.246-0.2546-0.0667-0.00160.31940.03280.04750.2346-0.01370.302764.22419.47333.557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )L1 - 25
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 79 )L26 - 79
3X-RAY DIFFRACTION3chain 'L' and (resid 80 through 117 )L80 - 117
4X-RAY DIFFRACTION4chain 'L' and (resid 118 through 132 )L118 - 132
5X-RAY DIFFRACTION5chain 'L' and (resid 133 through 154 )L133 - 154
6X-RAY DIFFRACTION6chain 'L' and (resid 155 through 178 )L155 - 178
7X-RAY DIFFRACTION7chain 'L' and (resid 179 through 216 )L179 - 216
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 33 )H1 - 33
9X-RAY DIFFRACTION9chain 'H' and (resid 34 through 76 )H34 - 76
10X-RAY DIFFRACTION10chain 'H' and (resid 77 through 91 )H77 - 91
11X-RAY DIFFRACTION11chain 'H' and (resid 92 through 127 )H92 - 127
12X-RAY DIFFRACTION12chain 'H' and (resid 128 through 153 )H128 - 153
13X-RAY DIFFRACTION13chain 'H' and (resid 154 through 221 )H154 - 221
14X-RAY DIFFRACTION14chain 'A' and (resid 1 through 117 )A1 - 117
15X-RAY DIFFRACTION15chain 'A' and (resid 118 through 216 )A118 - 216
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 76 )B1 - 76
17X-RAY DIFFRACTION17chain 'B' and (resid 77 through 91 )B77 - 91
18X-RAY DIFFRACTION18chain 'B' and (resid 92 through 142 )B92 - 142
19X-RAY DIFFRACTION19chain 'B' and (resid 143 through 221 )B143 - 221

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