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- PDB-4x7t: Structure of Omalizumab Fab fragment, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 4x7t
TitleStructure of Omalizumab Fab fragment, crystal form 2
Components
  • Omalizumab-Fab Heavy chain
  • Omalizumab-Fab Light chain
KeywordsIMMUNE SYSTEM / Antibody Fab Fragment / Anti-IgE antibody / Anti-inflammatory
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJensen, R.K. / Andersen, G.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Danish Natural Science Research Council Denmark
DanScatt Denmark
Novo Nordisk Foundation, Hallas-Mooller Fellowship Denmark
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the omalizumab Fab
Authors: Jensen, R.K. / Plum, M. / Tjerrild, L. / Jakob, T. / Spillner, E. / Andersen, G.R.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Omalizumab-Fab Heavy chain
L: Omalizumab-Fab Light chain
A: Omalizumab-Fab Heavy chain
B: Omalizumab-Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3436
Polymers95,1514
Non-polymers1922
Water00
1
H: Omalizumab-Fab Heavy chain
L: Omalizumab-Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6723
Polymers47,5762
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-38 kcal/mol
Surface area19580 Å2
MethodPISA
2
A: Omalizumab-Fab Heavy chain
B: Omalizumab-Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6723
Polymers47,5762
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-39 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.470, 73.490, 87.040
Angle α, β, γ (deg.)90.00, 116.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Omalizumab-Fab Heavy chain


Mass: 23653.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Omalizumab-Fab Light chain


Mass: 23922.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, Polyvinyl Pyrrolidone K15, Lithium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97551 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97551 Å / Relative weight: 1
ReflectionResolution: 3→45.41 Å / Num. obs: 19417 / % possible obs: 99.37 % / Redundancy: 3.4 % / Rsym value: 0.202 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.107 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.11 / % possible all: 99.32

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1593)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X7S

4x7s


Resolution: 3→45.408 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1957 10.08 %
Rwork0.1927 --
obs0.1972 19410 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→45.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 10 0 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046878
X-RAY DIFFRACTIONf_angle_d1.0739354
X-RAY DIFFRACTIONf_dihedral_angle_d13.2962436
X-RAY DIFFRACTIONf_chiral_restr0.041038
X-RAY DIFFRACTIONf_plane_restr0.0051200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.07520.38271420.34411211X-RAY DIFFRACTION99
3.0752-3.15830.37151360.30071254X-RAY DIFFRACTION99
3.1583-3.25120.29941300.27951244X-RAY DIFFRACTION99
3.2512-3.35610.31951460.26611223X-RAY DIFFRACTION99
3.3561-3.4760.2821280.24641232X-RAY DIFFRACTION98
3.476-3.61520.28321490.23941218X-RAY DIFFRACTION99
3.6152-3.77960.24951350.21441267X-RAY DIFFRACTION100
3.7796-3.97880.24881430.19851220X-RAY DIFFRACTION100
3.9788-4.22790.23091460.18051243X-RAY DIFFRACTION100
4.2279-4.5540.18411370.15241280X-RAY DIFFRACTION100
4.554-5.01180.17091380.13511234X-RAY DIFFRACTION99
5.0118-5.73580.1771440.15051262X-RAY DIFFRACTION100
5.7358-7.22180.24531470.16471259X-RAY DIFFRACTION100
7.2218-45.4130.19171360.15161306X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6159 Å / Origin y: -3.0265 Å / Origin z: 18.1444 Å
111213212223313233
T0.3581 Å20.0185 Å2-0.0193 Å2-0.3811 Å2-0.0636 Å2--0.3532 Å2
L0.8619 °2-0.0649 °20.0533 °2-0.4145 °20.1204 °2--1.1327 °2
S0.0258 Å °0.0812 Å °0.0356 Å °0.017 Å °-0.1524 Å °0.088 Å °-0.0687 Å °-0.3711 Å °0.093 Å °
Refinement TLS groupSelection details: all

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