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- PDB-1s5i: Fab (LNKB-2) of monoclonal antibody to Human Interleukin-2, cryst... -

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Basic information

Entry
Database: PDB / ID: 1s5i
TitleFab (LNKB-2) of monoclonal antibody to Human Interleukin-2, crystal structure
Components(Fab-fragment of monoclonal antibody) x 2
KeywordsIMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / x-ray analysis
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig gamma-1 chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPletnev, V.Z. / Goryacheva, E.A. / Tsygannik, I.N. / Nesmeyanov, V.A. / Pletnev, S.V. / Pangborn, W. / Duax, W.
Citation
Journal: Bioorg. Khim.
Title: [A new crystal form of the Fab fragment of a monoclonal antibody to human interleukin-2: the three-dimensional structure at 2.7 A resolution].
Authors: Pletnev, V.Z. / Goriacheva, E.A. / Tsygannik, I.N. / Nesmeianov, V.A. / Pletnev, S.V. / Pangborn, W. / Daux, W.
#1: Journal: Bioorg.Khim. / Year: 2000
Title: Spatial structure of a Fab-fragment of a monoclonal antibody to human interleukin-2 in two crystalline forms at a resolution of 2.2 and 2.9 angstroms
Authors: Fokin, A.V. / Afonin, P.V. / Mikhailova, I.Y. / Tsygannik, I.N. / Mareeva, T.Y. / Nesmeyanov, V.A. / Pangborn, W. / Lee, N. / Duax, W. / Siszak, E. / Pletnev, V.Z.
#2: Journal: Protein Sci. / Year: 2001
Title: Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide
Authors: Afonin, P.V. / Fokin, A.V. / Tsygannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Michaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Pangborn, W. / Duax, W. / Pletnev, V.Z.
History
DepositionJan 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.5Aug 23, 2023Group: 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
Remark 999SEQUENCE The sequence of this protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab-fragment of monoclonal antibody
H: Fab-fragment of monoclonal antibody


Theoretical massNumber of molelcules
Total (without water)48,0742
Polymers48,0742
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-24 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.816, 90.682, 139.819
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 Fab-fragment of monoclonal antibody


Mass: 24203.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma
#2: Antibody Fab-fragment of monoclonal antibody


Mass: 23869.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: hybridoma / References: UniProt: P01869
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.87 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG-8000, ZnAc, NaN3, Na(CH3)2AsO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→41.5 Å / Num. all: 14370 / Num. obs: 14370 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Num. unique all: 879 / % possible all: 88.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F8T

1f8t


Resolution: 2.7→41.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cross validation maximum likelihood simulated annealing refinement (CNS package)
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1462 -RANDOM
Rwork0.2 ---
all0.205 ---
obs0.275 14370 92 %-
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--15.997 Å20 Å20 Å2
2--3.347 Å20 Å2
3---12.65 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å / Luzzati sigma a obs: 0.55 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 66 3447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_torsion_deg27.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.95
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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