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- PDB-2xa8: Crystal structure of the Fab domain of omalizumab at 2.41A -

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Basic information

Entry
Database: PDB / ID: 2xa8
TitleCrystal structure of the Fab domain of omalizumab at 2.41A
Components
  • OMALIZUMAB HEAVY CHAIN
  • OMALIZUMAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / XOLAIR / ALLERGY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsHuang, C.H. / Hung, F.H.A. / Lim, C. / Chang, T.W. / Ma, C.
CitationJournal: Sci Rep / Year: 2015
Title: Structural and Physical Basis for Anti-IgE Therapy.
Authors: Wright, J.D. / Chu, H.M. / Huang, C.H. / Ma, C. / Chang, T.W. / Lim, C.
History
DepositionMar 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Version format compliance
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / reflns
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: OMALIZUMAB HEAVY CHAIN
L: OMALIZUMAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,2202
Polymers47,2202
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25.6 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.600, 73.851, 141.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody OMALIZUMAB HEAVY CHAIN


Mass: 23297.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#2: Antibody OMALIZUMAB LIGHT CHAIN


Mass: 23922.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.57 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M AMMONIUM SULFATE, 0.1 M NA HEPES PH 7.5, 2% W/V PEG400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1
DetectorType: BRUKER / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→30 Å / Num. obs: 25869 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.43 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.3_473)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL5

2vl5


Resolution: 2.42→36.93 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.9 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.269 1310 5.1 %
Rwork0.221 --
obs0.223 25778 97.7 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.55 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-14.66 Å20 Å20 Å2
2---5.22 Å20 Å2
3----9.44 Å2
Refinement stepCycle: LAST / Resolution: 2.42→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 72 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063410
X-RAY DIFFRACTIONf_angle_d0.9784638
X-RAY DIFFRACTIONf_dihedral_angle_d14.9521206
X-RAY DIFFRACTIONf_chiral_restr0.066516
X-RAY DIFFRACTIONf_plane_restr0.008596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4234-2.52040.46961180.39542435X-RAY DIFFRACTION88
2.5204-2.63510.33931380.32032683X-RAY DIFFRACTION98
2.6351-2.77390.37521400.28192703X-RAY DIFFRACTION99
2.7739-2.94770.30581670.24122720X-RAY DIFFRACTION100
2.9477-3.17510.30411560.22322737X-RAY DIFFRACTION100
3.1751-3.49450.22941540.2052740X-RAY DIFFRACTION99
3.4945-3.99960.27171520.20612747X-RAY DIFFRACTION99
3.9996-5.0370.22361550.17332766X-RAY DIFFRACTION98
5.037-36.92980.23771300.21812937X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 60.5155 Å / Origin y: 40.2083 Å / Origin z: 16.6056 Å
111213212223313233
T0.178 Å2-0.0508 Å20.006 Å2-0.2221 Å2-0.0069 Å2--0.2122 Å2
L0.3008 °2-0.0206 °20.0148 °2-0.9529 °2-0.4878 °2--0.7282 °2
S-0.0369 Å °0.0323 Å °0.0319 Å °-0.1029 Å °0.0778 Å °0.092 Å °0.1388 Å °-0.0777 Å °0 Å °
Refinement TLS groupSelection details: ALL

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