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- PDB-1f8t: FAB (LNKB-2) OF MONOCLONAL ANTIBODY, CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1f8t
TitleFAB (LNKB-2) OF MONOCLONAL ANTIBODY, CRYSTAL STRUCTURE
Components
  • ANTIBODY FAB FRAGMENT (HEAVY CHAIN)
  • ANTIBODY FAB FRAGMENT (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / monoclonal antibody / antigen-binding fragment / interleukin-2 / x-ray analysis / crystal
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsFokin, A.V. / Afonin, P.V. / Mikhailova, I.I. / Tsygannik, I.N. / Mareeva, T.I.
CitationJournal: 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.I.u. / Tsygannik, I.N. / Mareeva, T.I.u. / Nesmeianov, V.A. / Pangborn, W. / Lee, N. / Duax, W. / Siszak, E. / Pletnev, V.Z.
History
DepositionJul 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 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 1.4Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTIBODY FAB FRAGMENT (LIGHT CHAIN)
H: ANTIBODY FAB FRAGMENT (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)48,0582
Polymers48,0582
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-24 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.24, 72.01, 86.99
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ANTIBODY FAB FRAGMENT (LIGHT CHAIN)


Mass: 24203.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody ANTIBODY FAB FRAGMENT (HEAVY CHAIN)


Mass: 23853.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
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

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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 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→99 Å / Num. all: 22492 / Num. obs: 21459 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.1935 / Num. unique all: 3156 / % possible all: 94.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.9refinement
X-PLORphasing
RefinementResolution: 2.2→99 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Cross-validated maximum likelihood simulated annealing refinement (CNS package)
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2116 -Random
Rwork0.171 ---
all-23673 --
obs-22492 95 %-
Refinement stepCycle: LAST / Resolution: 2.2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 0 213 3593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.84

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