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- PDB-6tcn: Crystal structure of the omalizumab Fab - crystal form II -

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Basic information

Entry
Database: PDB / ID: 6tcn
TitleCrystal structure of the omalizumab Fab - crystal form II
Components(Omalizumab Fab) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / immunoglobulin
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
H: Omalizumab Fab
A: Omalizumab Fab
B: Omalizumab Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,20317
Polymers97,1904
Non-polymers1,01313
Water4,432246
1
L: Omalizumab Fab
H: Omalizumab Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,32712
Polymers48,5952
Non-polymers73310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-36 kcal/mol
Surface area18780 Å2
MethodPISA
2
A: Omalizumab Fab
B: Omalizumab Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8755
Polymers48,5952
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-39 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.295, 73.569, 87.098
Angle α, β, γ (deg.)90.000, 116.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody Omalizumab Fab


Mass: 23922.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Omalizumab Fab light chain / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#2: Antibody Omalizumab Fab


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)

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Non-polymers , 5 types, 259 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M phosphate-citrate pH4.2, 20% PEG 1000 and 0.2M lithium sulphate. Cryoprotected with 0.1M sodium acetate pH4.6, 25% PEG 4000 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 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→77.893 Å / Num. obs: 42827 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6015 / Rpim(I) all: 0.454 / % possible all: 96.9

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Processing

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

6tcm


Resolution: 2.3→77.893 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.28
RfactorNum. reflection% reflection
Rfree0.2258 2151 5.03 %
Rwork0.1878 --
obs0.1897 42804 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.53 Å2 / Biso mean: 47.449 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: final / Resolution: 2.3→77.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 62 246 6766
Biso mean--62.02 41.26 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026689
X-RAY DIFFRACTIONf_angle_d0.5359116
X-RAY DIFFRACTIONf_chiral_restr0.0431014
X-RAY DIFFRACTIONf_plane_restr0.0041164
X-RAY DIFFRACTIONf_dihedral_angle_d12.23925
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35350.3281260.286251494
2.3535-2.41240.2981490.2633265499
2.4124-2.47760.29611400.25162744100
2.4776-2.55050.27451480.24162690100
2.5505-2.63290.28751340.23562718100
2.6329-2.7270.23491500.2332721100
2.727-2.83620.27271390.22732725100
2.8362-2.96520.28631400.22182696100
2.9652-3.12160.26831420.21712720100
3.1216-3.31720.26541360.20992742100
3.3172-3.57330.25811420.18332714100
3.5733-3.93290.18851500.16212732100
3.9329-4.50190.18021600.14352729100
4.5019-5.67170.16151470.13342751100
5.6717-77.8930.19181480.1682803100
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)
10.87641.48-0.8263.466-1.07411.36520.11640.0685-0.02820.50460.0006-0.1854-0.19220.0423-0.10110.2513-0.0238-0.0260.2420.04750.270339.7169-2.685917.0585
21.80141.15170.30520.89030.32512.1761-0.07330.0211-0.3285-0.0356-0.0975-0.20170.19080.13750.13390.20250.03690.05730.2080.04050.300938.9786-12.34039.2214
31.41090.3051-0.50031.6716-0.04240.8623-0.06040.1354-0.093-0.1254-0.092-0.37540.07930.10980.12760.2441-0.0083-0.00070.23180.06320.258541.1387-8.08889.4763
41.1647-1.15370.17832.78910.05932.3744-0.41850.28821.3652-0.1936-0.38550.55930.1323-0.6669-0.93890.02670.1557-0.31130.11260.25690.804935.933513.842810.0856
52.7512-0.17470.21122.07320.28861.1387-0.10620.0540.8010.0384-0.2502-0.0649-0.3516-0.20050.23690.38650.1496-0.05740.48060.06020.628215.439321.04764.6666
63.3703-0.8712-0.01551.71090.27331.6454-0.2643-0.00650.020.3728-0.1872-0.0329-0.2182-0.16090.35160.39090.02460.00980.44680.05620.385821.226316.90198.7606
70.5986-0.4072-0.66921.05410.09060.7582-0.5792-0.69870.97050.44720.1982-0.0572-0.2415-0.47390.12170.51250.2311-0.17260.5024-0.08710.843912.50726.84267.4289
81.0705-1.0470.10471.86340.39740.86910.27350.3645-0.1947-0.2507-0.34270.28140.0701-0.29390.04870.29920.0286-0.01690.4245-0.13320.392821.558-16.6701-3.8635
91.4220.52240.39780.9533-1.1081.8950.01550.0616-0.37550.2288-0.19990.31110.0426-0.28410.16030.21920.02340.05390.2689-0.05980.347826.1346-19.74615.7713
102.2650.16780.42361.8672-0.17771.98830.02870.0624-0.4170.0324-0.33240.36590.537-0.19570.18340.3225-0.04470.03370.3771-0.18660.501919.9718-23.18711.2219
112.1336-0.2967-0.84811.24360.53710.8595-0.0126-0.0365-0.33650.0325-0.0760.25290.4461-0.0780.12880.27530.00290.05040.3299-0.09970.3718.5392-13.93986.829
120.9838-0.6477-0.20081.40330.50230.39590.09550.2633-0.0602-0.2109-0.15630.08820.0275-0.2150.08230.23880.07630.02240.3725-0.03910.286622.1675-5.38440.3876
131.08050.5566-0.37472.9958-0.76571.35430.18170.13720.1773-0.6304-0.48540.0182-0.04890.07590.16910.3680.14840.04170.57050.1350.462415.1378.9335-3.7328
141.01390.29020.74252.33660.56871.26190.20470.37870.197-0.3581-0.3442-0.0389-0.2545-0.01870.1250.34230.17650.09380.49870.19610.393417.333111.3646-4.1917
151.85310.33010.14430.53680.9411.8190.03050.35560.1907-0.7026-0.22990.26060.0408-0.17390.11610.58980.180.02960.57020.0690.453711.023112.1645-11.6746
161.17830.3940.21042.874-0.55721.69810.07260.34730.0242-0.5523-0.169-0.0368-0.1502-0.3980.09510.52170.09690.03880.3955-0.0130.238521.2322-2.504821.6694
173.0899-0.3979-0.36221.57880.07572.54330.2421-0.10010.5167-0.3416-0.48940.1515-0.32020.01640.18670.45760.02480.01660.2139-0.01340.308320.12246.744930.0648
181.4364-0.68880.58492.2310.85010.73710.1818-0.08570.09810.0054-0.2875-0.236-0.0908-0.07290.07880.4441-0.01020.07170.290.02770.269624.3722-0.244230.8703
190.4650.7960.05942.01770.57841.3809-0.0304-0.12420.04880.0756-0.09510.21810.0565-0.6060.07980.3798-0.0201-0.00320.4779-0.04090.32454.0332-15.971729.1423
201.8959-0.08241.25490.010.221.0291-0.0931-0.074-0.0606-0.0364-0.0495-0.00560.4449-0.45590.16510.4664-0.19980.0520.4525-0.0320.32142.461-23.679324.2219
211.05130.69251.011.18740.53210.841-0.0533-0.0574-0.42850.05630.06570.06370.4946-0.5505-0.08580.5755-0.31230.05130.6165-0.090.4404-5.27-31.286625.0886
221.04960.69360.19321.6050.30141.46010.29210.225-0.14420.0452-0.42680.53760.1461-0.58810.1410.45540.0717-0.07830.5462-0.27860.48371.655110.789141.4768
231.3499-0.5126-0.18491.68880.52661.4233-0.04840.1559-0.0158-0.3387-0.37150.5359-0.3566-0.62080.28950.45430.1114-0.12620.4107-0.1930.41995.101612.812834.3428
241.83720.55220.26041.29480.24111.43720.0414-1.04060.29480.5191-0.23670.30.3156-0.660.16790.5449-0.17730.09581.0053-0.23790.4223-6.0517-17.651439.3157
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 52 )L26 - 52
3X-RAY DIFFRACTION3chain 'L' and (resid 53 through 105 )L53 - 105
4X-RAY DIFFRACTION4chain 'L' and (resid 106 through 117 )L106 - 117
5X-RAY DIFFRACTION5chain 'L' and (resid 118 through 154 )L118 - 154
6X-RAY DIFFRACTION6chain 'L' and (resid 155 through 178 )L155 - 178
7X-RAY DIFFRACTION7chain 'L' and (resid 179 through 217 )L179 - 217
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 33 )H1 - 33
9X-RAY DIFFRACTION9chain 'H' and (resid 34 through 60 )H34 - 60
10X-RAY DIFFRACTION10chain 'H' and (resid 61 through 83 )H61 - 83
11X-RAY DIFFRACTION11chain 'H' and (resid 84 through 98 )H84 - 98
12X-RAY DIFFRACTION12chain 'H' and (resid 99 through 142 )H99 - 142
13X-RAY DIFFRACTION13chain 'H' and (resid 143 through 165 )H143 - 165
14X-RAY DIFFRACTION14chain 'H' and (resid 166 through 211 )H166 - 211
15X-RAY DIFFRACTION15chain 'H' and (resid 212 through 222 )H212 - 222
16X-RAY DIFFRACTION16chain 'A' and (resid 1 through 25 )A1 - 25
17X-RAY DIFFRACTION17chain 'A' and (resid 26 through 52 )A26 - 52
18X-RAY DIFFRACTION18chain 'A' and (resid 53 through 94 )A53 - 94
19X-RAY DIFFRACTION19chain 'A' and (resid 95 through 143 )A95 - 143
20X-RAY DIFFRACTION20chain 'A' and (resid 144 through 176 )A144 - 176
21X-RAY DIFFRACTION21chain 'A' and (resid 177 through 217 )A177 - 217
22X-RAY DIFFRACTION22chain 'B' and (resid 1 through 33 )B1 - 33
23X-RAY DIFFRACTION23chain 'B' and (resid 34 through 119 )B34 - 119
24X-RAY DIFFRACTION24chain 'B' and (resid 120 through 221 )B120 - 221

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