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- PDB-6tcm: Crystal structure of the omalizumab Fab - crystal form I -

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Basic information

Entry
Database: PDB / ID: 6tcm
TitleCrystal structure of the omalizumab Fab - crystal form I
Components(Omalizumab Fab) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Revision 1.2Nov 13, 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: Omalizumab Fab
H: Omalizumab Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,64013
Polymers48,5952
Non-polymers1,04511
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-46 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.375, 73.555, 141.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Omalizumab Fab


Mass: 23922.287 Da / Num. of mol.: 1
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.: 1
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 , 4 types, 325 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.57 Å3/Da / Density % sol: 65.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085M Tris pH8.5, 42.5% MPD, 15% glycerol and 0.17M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→65.38 Å / Num. obs: 58932 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.078 / Net I/σ(I): 4.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.641 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3588 / CC1/2: 0.413 / Rpim(I) all: 1.101 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FJF

2fjf


Resolution: 1.85→65.224 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.1903 2899 5 %
Rwork0.1677 --
obs0.1688 57943 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.91 Å2 / Biso mean: 29.315 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.85→65.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 70 314 3685
Biso mean--54.22 40.07 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143520
X-RAY DIFFRACTIONf_angle_d1.3344816
X-RAY DIFFRACTIONf_chiral_restr0.085539
X-RAY DIFFRACTIONf_plane_restr0.008607
X-RAY DIFFRACTIONf_dihedral_angle_d13.3332109
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.88040.40021230.3702235590
1.8804-1.91280.27621270.2779240291
1.9128-1.94760.25361300.2338245594
1.9476-1.98510.21791340.1929254996
1.9851-2.02560.20271330.1854252398
2.0256-2.06960.25551380.184263099
2.0696-2.11780.19151380.18272627100
2.1178-2.17070.20851390.17082632100
2.1707-2.22940.20511390.17042642100
2.2294-2.2950.21461390.17932638100
2.295-2.36910.22481380.16382626100
2.3691-2.45380.19611410.16642672100
2.4538-2.5520.19211380.1712633100
2.552-2.66820.2291390.17742646100
2.6682-2.80890.26141420.21072660100
2.8089-2.98480.19271410.1522684100
2.9848-3.21530.17891390.15342661100
3.2153-3.53890.13941430.14042687100
3.5389-4.05090.15881420.13562707100
4.0509-5.10340.13521440.12442742100
5.1034-65.2240.18411520.18382873100
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)
10.31270.17950.16290.260.30210.33590.0351-0.01610.0304-0.10060.0584-0.2088-0.0560.34620.020.12990.0470.00980.2426-0.010.256317.4242-0.2198-31.6521
20.4940.4204-0.01240.3547-0.29270.24170.08310.15570.0465-0.0081-0.0415-0.07340.15420.03870.03110.15260.0628-0.00090.1478-0.03230.1519.4398-9.9793-31.683
30.10830.13190.33330.78280.34390.79930.02080.0147-0.0164-0.0647-0.0032-0.0317-0.00920.06570.00140.10810.02520.01060.1666-0.0010.19777.9412.9974-26.7173
40.33750.10620.0730.2184-0.14160.1954-0.06090.0240.09780.04430.0143-0.07220.05430.0718-0.00670.1710.015-0.02150.1902-0.03240.1649.0720.4493-12.1409
50.12390.38380.16140.19520.27740.137-0.0815-0.06290.17530.06360.01060.0197-0.1822-0.0628-0.07410.2120.0243-0.03950.2117-0.07040.21568.562828.2851-4.3152
60.0695-0.12490.03010.16240.02820.1778-0.0205-0.1028-0.0270.395-0.06730.14250.2804-0.2444-0.01970.33990.01440.00510.245-0.00670.1855-4.174-14.4093-14.4926
70.3538-0.28120.08210.2560.07470.63820.1022-0.0873-0.07710.4301-0.0032-0.10140.35320.01840.00190.28380.033-0.03920.1472-0.00070.15364.3256-18.9648-16.8523
80.0263-0.04960.04870.27950.27430.2704-0.0446-0.1586-0.02910.89670.00520.17450.5856-0.1229-0.08010.50920.068-0.13220.24860.00230.11464.3019-15.9633-8.6299
90.2611-0.1445-0.12910.33550.13060.8593-0.036-0.03540.05690.25410.06330.00990.15450.00490.00250.12280.0338-0.00590.1408-0.0140.1522-1.02092.8016-12.1342
100.50190.1435-0.37290.41540.03530.3277-0.03890.01440.0120.16780.07350.0832-0.0261-0.0837-00.16220.0375-0.00050.19810.0030.1869-6.014814.1059-7.9642
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 132 )L53 - 132
4X-RAY DIFFRACTION4chain 'L' and (resid 133 through 178 )L133 - 178
5X-RAY DIFFRACTION5chain 'L' and (resid 179 through 217 )L179 - 217
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 33 )H1 - 33
7X-RAY DIFFRACTION7chain 'H' and (resid 34 through 76 )H34 - 76
8X-RAY DIFFRACTION8chain 'H' and (resid 77 through 91 )H77 - 91
9X-RAY DIFFRACTION9chain 'H' and (resid 92 through 165 )H92 - 165
10X-RAY DIFFRACTION10chain 'H' and (resid 166 through 222 )H166 - 222

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