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- PDB-6tcs: Crystal structure of the omalizumab scFv -

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Basic information

Entry
Database: PDB / ID: 6tcs
TitleCrystal structure of the omalizumab scFv
ComponentsOmalizumab scFv
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
Revision 1.2Oct 9, 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

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Assembly

Deposited unit
A: Omalizumab scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7022
Polymers29,5961
Non-polymers1061
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint6 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.909, 73.909, 117.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1375-

HOH

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Components

#1: Antibody Omalizumab scFv


Mass: 29596.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Omalizumab scFv / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate pH5.6, 15% PEG 4000 and 0.2M ammonium sulphate. Crystals were cryoprotected with 0.1M tri-sodium citrate pH5.6, 30% PEG 4000 and 0.2M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.3→64.01 Å / Num. obs: 17055 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.121 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 2.248 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1655 / CC1/2: 0.597 / Rpim(I) all: 1.064 / % possible all: 99.9

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Processing

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

6tcm


Resolution: 2.3→56.237 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.2062 843 4.99 %
Rwork0.178 --
obs0.1794 16902 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.85 Å2 / Biso mean: 33.9248 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 2.3→56.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 14 78 1831
Biso mean--53.2 38.72 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041816
X-RAY DIFFRACTIONf_angle_d0.6832478
X-RAY DIFFRACTIONf_chiral_restr0.046269
X-RAY DIFFRACTIONf_plane_restr0.003315
X-RAY DIFFRACTIONf_dihedral_angle_d14.2361057
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3002-2.44430.28111360.2175261698
2.4443-2.6330.23021370.2066263999
2.633-2.8980.21951410.1869265299
2.898-3.31730.20021340.1781267699
3.3173-4.17920.22221390.1834265198
4.1792-56.2370.16771560.1514282599
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)
13.62330.35791.61590.5847-0.33791.7982-0.1296-0.5769-0.20.23550.10620.22520.1042-0.25950.00830.19740.07630.03130.3611-0.07220.1518-50.825328.9737-2.4157
22.4904-1.0849-0.01841.07730.25661.7547-0.052-0.06580.28540.052-0.0722-0.0209-0.12150.11170.09850.12710.035-0.01220.1653-0.02010.174-42.8930.7514-9.0202
30.78520.1868-0.94510.76940.26331.4638-0.07680.24-0.0793-0.1836-0.02190.06630.2432-0.30450.00730.2081-0.0310.00240.1945-0.02860.1963-46.129115.302-17.4898
41.48630.04320.02322.3644-0.17451.5914-0.086-0.0702-0.10770.15770.10660.05710.32920.26480.0050.20830.03850.04810.14610.00890.1526-33.439813.7006-15.6985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 105 )A19 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 1012 )A106 - 1012
4X-RAY DIFFRACTION4chain 'A' and (resid 1013 through 1121 )A1013 - 1121

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