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- PDB-1f90: FAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERL... -

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Basic information

Entry
Database: PDB / ID: 1f90
TitleFAB FRAGMENT OF MONOCLONAL ANTIBODY (LNKB-2) AGAINST HUMAN INTERLEUKIN-2 IN COMPLEX WITH ANTIGENIC PEPTIDE
Components
  • (FAB FRAGMENT OF MONOCLONAL ANTIBODY) x 2
  • ANTIGENIC NONAPEPTIDE
KeywordsIMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / antigenic peptide
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsAfonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. ...Afonin, P.V. / Fokin, A.V. / Tsigannik, I.N. / Mikhailova, I.Y. / Onoprienko, L.V. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Duax, W.L. / Pletnev, V.Z.
Citation
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. / Mikhaleva, I.I. / Ivanov, V.T. / Mareeva, T.Y. / Nesmeyanov, V.A. / Li, N. / Pangborn, W.A. / Duax, W.L. / Pletnev, V.Z.
#1: Journal: BIOORG.KHIM. / Year: 2000
Title: THREE-DIMENSIONAL STRUCTURE OF ANTIGEN BINDING FRAGMENT OF MONOCLONAL ANTIBODY AGAINST HUMAN INTERLEUKIN-2 IN TWO CRYSTAL FORMS AT 2.2 AND 2.9 A RESOLUTION.
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. / Sijak, E. / Pletnev, V.Z.
History
DepositionJul 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was ...SEQUENCE The sequence of the protein has not been deposited in any sequence database. It was published in the Bioorganicheskaya Khimiya (Rus) (1995), V21, N6, p430-435. "Cloning cDNA Encoding Fv-Fragments of the Light and Heavy Chains of the Monoclonal Antibody" by A.I.Paskhin, T.N. Golovina, V.A. Nesmeyanov, V.G. Korobko.

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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
E: ANTIGENIC NONAPEPTIDE


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers49,1133
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-27 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.83, 72.76, 72.15
Angle α, β, γ (deg.)90.0, 106.98, 90.0
Int Tables number4
Space group name H-MP1211

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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: 23853.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA
#3: Protein/peptide ANTIGENIC NONAPEPTIDE


Mass: 1055.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthetized in Solution
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-4000, 2-propanol, Na-citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-7 mg/mlprotein1drop
212-13 %PEG40001reservoir
312-13 %2-propanol1reservoir
460 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 13733 / Num. obs: 11984 / % possible obs: 83.4 % / Observed criterion σ(F): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5825 / Num. unique all: 1850 / % possible all: 97.15
Reflection
*PLUS
Num. obs: 9377 / % possible obs: 99.7 % / Num. measured all: 19271 / Rmerge(I) obs: 0.112

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.9refinement
X-PLORphasing
RefinementResolution: 2.6→99 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Cross-validated maximum likelihood simulated annealing refinement (CNS package)
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1212 -Random
Rwork0.165 ---
all-14376 --
obs-13733 95.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 0 267 4514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg27.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.85
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 99 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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