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- PDB-3i9g: Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragm... -

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Basic information

Entry
Database: PDB / ID: 3i9g
TitleCrystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate
Components(Sonepcizumab antibody Fab fragment, ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Fab / Sphingosine-1-phosphate / Calcium / Immunoglobin / IgG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-S1P
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHuxford, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen.
Authors: Wojciak, J.M. / Zhu, N. / Schuerenberg, K.T. / Moreno, K. / Shestowsky, W.S. / Hiraiwa, M. / Sabbadini, R. / Huxford, T.
#1: Journal: J.Lipid Res. / Year: 2009
Title: Production and characterization of monoclonal anti-sphingosine-1-phosphate antibodies
Authors: O'Brien, N. / Jones, S.T. / Williams, D.G. / Cunningham, H.B. / Moreno, K. / Visentin, B. / Gentile, A. / Vekich, J. / Shestowsky, W. / Hiraiwa, M. / Matteo, R. / Cavalli, A. / Grotjahn, D. ...Authors: O'Brien, N. / Jones, S.T. / Williams, D.G. / Cunningham, H.B. / Moreno, K. / Visentin, B. / Gentile, A. / Vekich, J. / Shestowsky, W. / Hiraiwa, M. / Matteo, R. / Cavalli, A. / Grotjahn, D. / Grant, M. / Hansen, G. / Campbell, M.A. / Sabbadini, R.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Sonepcizumab antibody Fab fragment, heavy chain
L: Sonepcizumab antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,05110
Polymers47,4702
Non-polymers5818
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-83 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.052, 70.889, 138.719
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 HL

#1: Antibody Sonepcizumab antibody Fab fragment, heavy chain


Mass: 24027.127 Da / Num. of mol.: 1 / Fragment: Fab Fragment
Source method: isolated from a genetically manipulated source
Details: Humanized mouse IgG1K expressed from a stable transfected CHO cell line
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG1K / Cell line (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Sonepcizumab antibody Fab fragment, light chain


Mass: 23442.965 Da / Num. of mol.: 1 / Fragment: Fab Fragment
Source method: isolated from a genetically manipulated source
Details: Humanized mouse IgG1K expressed from a stable transfected CHO cell line
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO cells / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 291 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-S1P / (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate / sphingosine 1-phosphate


Mass: 379.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38NO5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium ...Details: 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium citrate (pH 6.0) and 10% (v/v) ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 52056 / Num. obs: 50494 / % possible obs: 97 % / Observed criterion σ(I): 3.8 / Redundancy: 5.1 % / Rsym value: 0.055 / Net I/σ(I): 26.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.18 / Num. unique all: 3940 / Rsym value: 0.409 / % possible all: 76.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 2.81 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2548 5.1 %RANDOM
Rwork0.19 ---
obs0.192 50430 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.32 Å2 / Biso mean: 28.232 Å2 / Biso min: 14.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 32 283 3676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223471
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9544715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8495433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92124.752141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26415567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6121511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022595
X-RAY DIFFRACTIONr_nbd_refined0.1940.21442
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2287
X-RAY DIFFRACTIONr_metal_ion_refined0.2230.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.213
X-RAY DIFFRACTIONr_mcbond_it0.9131.52235
X-RAY DIFFRACTIONr_mcangle_it1.50623527
X-RAY DIFFRACTIONr_scbond_it2.10231431
X-RAY DIFFRACTIONr_scangle_it3.374.51188
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 147 -
Rwork0.257 2601 -
all-2748 -
obs--72.83 %

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