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- PDB-4x7s: Structure of omalizumab Fab fragment crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4x7s
TitleStructure of omalizumab Fab fragment crystal form 1
Components
  • Epididymis luminal protein 214
  • Ig kappa chain C region
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: 1.9 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
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: Epididymis luminal protein 214
L: Ig kappa chain C region


Theoretical massNumber of molelcules
Total (without water)47,5762
Polymers47,5762
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-24 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.860, 73.410, 140.180
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 Epididymis luminal protein 214


Mass: 23653.387 Da / Num. of mol.: 1 / Fragment: residues 20-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-214 / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Ig kappa chain C region


Mass: 23922.287 Da / Num. of mol.: 1 / Fragment: residues 23-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.9→48.61 Å / Num. obs: 53406 / % possible obs: 99.77 % / Redundancy: 6.4 % / Rsym value: 0.088 / Net I/σ(I): 12.73
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.71 / % possible all: 98.52

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XA8

2xa8


Resolution: 1.9→48.606 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2703 5.06 %
Rwork0.1997 --
obs0.2013 53406 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 182 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043435
X-RAY DIFFRACTIONf_angle_d0.9314679
X-RAY DIFFRACTIONf_dihedral_angle_d12.4231222
X-RAY DIFFRACTIONf_chiral_restr0.032519
X-RAY DIFFRACTIONf_plane_restr0.004600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93460.42871240.43812581X-RAY DIFFRACTION98
1.9346-1.97180.39141410.40292617X-RAY DIFFRACTION100
1.9718-2.01210.36961530.36332621X-RAY DIFFRACTION100
2.0121-2.05580.35871240.33792648X-RAY DIFFRACTION100
2.0558-2.10360.32421380.3112642X-RAY DIFFRACTION100
2.1036-2.15620.3071510.27552632X-RAY DIFFRACTION100
2.1562-2.21450.27151560.26292622X-RAY DIFFRACTION100
2.2145-2.27970.27291470.2422642X-RAY DIFFRACTION100
2.2797-2.35330.3121180.23522667X-RAY DIFFRACTION100
2.3533-2.43740.28561540.23172653X-RAY DIFFRACTION100
2.4374-2.5350.25091280.2262687X-RAY DIFFRACTION100
2.535-2.65030.26431370.21232658X-RAY DIFFRACTION100
2.6503-2.790.21911420.20762651X-RAY DIFFRACTION100
2.79-2.96480.24511580.21282678X-RAY DIFFRACTION100
2.9648-3.19370.23051500.20922673X-RAY DIFFRACTION100
3.1937-3.5150.18481520.18632687X-RAY DIFFRACTION100
3.515-4.02340.23191480.16582708X-RAY DIFFRACTION100
4.0234-5.06830.16581550.13912733X-RAY DIFFRACTION100
5.0683-48.6220.23811270.18622903X-RAY DIFFRACTION100

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