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- PDB-3cfc: High-resolution structure of blue fluorescent antibody EP2-19G2 -

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Basic information

Entry
Database: PDB / ID: 3cfc
TitleHigh-resolution structure of blue fluorescent antibody EP2-19G2
Components
  • BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
  • BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / BLUE-FLUORESCENT ANTIBODY / HAPTEN COMPLEX / ELECTRON TRANSFER
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDebler, E.W. / Wilson, I.A.
CitationJournal: Science / Year: 2008
Title: Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex.
Authors: Debler, E.W. / Kaufmann, G.F. / Meijler, M.M. / Heine, A. / Mee, J.M. / Pljevaljcic, G. / Di Bilio, A.J. / Schultz, P.G. / Millar, D.P. / Janda, K.D. / Wilson, I.A. / Gray, H.B. / Lerner, R.A.
History
DepositionMar 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
L: BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9223
Polymers46,8292
Non-polymers921
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-25 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.891, 87.891, 114.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11H-348-

HOH

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Components

#1: Antibody BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN


Mass: 22746.715 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: PURIFIED FROM ASCITIC FLUID / Source: (natural) Mus musculus (house mouse)
Cell: HYBRIDOMA CELLS FROM 129GIX+ SPLEEN CELLS FUSED WITH BALB/C MYELOMA CELLS
#2: Antibody BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN


Mass: 24082.723 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: PURIFIED FROM ASCITIC FLUID / Source: (natural) Mus musculus (house mouse)
Cell: HYBRIDOMA CELLS FROM 129GIX+ SPLEEN CELLS FUSED WITH BALB/C MYELOMA CELLS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 47.7 %
Crystal growpH: 4.5
Details: 18% PEG 8000, 0.1M ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2005 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 49748 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 45.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.772 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0011refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FL3

1fl3


Resolution: 1.7→28.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.634 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2518 5.1 %RANDOM
Rwork0.191 ---
obs0.193 47209 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 6 332 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223464
X-RAY DIFFRACTIONr_bond_other_d0.0020.022321
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.964737
X-RAY DIFFRACTIONr_angle_other_deg0.9123.0045681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03123.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.651517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023905
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02688
X-RAY DIFFRACTIONr_nbd_refined0.1920.2524
X-RAY DIFFRACTIONr_nbd_other0.210.22318
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21691
X-RAY DIFFRACTIONr_nbtor_other0.0880.21933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2371.52836
X-RAY DIFFRACTIONr_mcbond_other0.261.5897
X-RAY DIFFRACTIONr_mcangle_it1.45423636
X-RAY DIFFRACTIONr_scbond_it2.32831469
X-RAY DIFFRACTIONr_scangle_it3.0914.51101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 181 -
Rwork0.243 3414 -
obs--99.89 %

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