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- PDB-3cfb: High-resolution structure of blue fluorescent antibody EP2-19G2 i... -

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Basic information

Entry
Database: PDB / ID: 3cfb
TitleHigh-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene hapten at 100K
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 / 4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Advisory / 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 30, 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
L: BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
H: BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
A: BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
B: BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,83212
Polymers93,6614
Non-polymers1,1718
Water10,629590
1
A: BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
B: BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4166
Polymers46,8302
Non-polymers5864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-27.4 kcal/mol
Surface area19380 Å2
MethodPISA
2
L: BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN
H: BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4166
Polymers46,8302
Non-polymers5864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-22.3 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.707, 61.015, 92.246
Angle α, β, γ (deg.)90.00, 116.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN


Mass: 24082.723 Da / Num. of mol.: 2 / 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-IGG2B HEAVY CHAIN


Mass: 22747.699 Da / Num. of mol.: 2 / 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-SPB / 4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID / 5-OXO-5-({4-[(E)-2-PHENYLVINYL]PHENYL}AMINO)PENTANOIC ACID / N-(TRANS-4-STILBENYL)-5-AMINO-5-OXO-PENTANOIC ACID


Mass: 309.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growpH: 5.5
Details: 20% PEG 4000, 0.2M KSCN, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97622
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 10, 2005 / Details: MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 121549 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 58.9 Å2 / Rsym value: 0.052 / Net I/σ(I): 30.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.704 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0017refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FL3

1fl3


Resolution: 1.6→42.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.116 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6274 5 %RANDOM
Rwork0.186 ---
obs0.187 118453 97.3 %-
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: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å2-0.09 Å2
2---0.4 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 82 590 7234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227058
X-RAY DIFFRACTIONr_bond_other_d0.0030.024733
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.979652
X-RAY DIFFRACTIONr_angle_other_deg0.9113.00311582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38323.701254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5981535
X-RAY DIFFRACTIONr_chiral_restr0.0950.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027983
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021418
X-RAY DIFFRACTIONr_nbd_refined0.2010.21173
X-RAY DIFFRACTIONr_nbd_other0.2050.24840
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23458
X-RAY DIFFRACTIONr_nbtor_other0.0860.23980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1090.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2121.55723
X-RAY DIFFRACTIONr_mcbond_other0.2481.51806
X-RAY DIFFRACTIONr_mcangle_it1.41927349
X-RAY DIFFRACTIONr_scbond_it2.3733061
X-RAY DIFFRACTIONr_scangle_it3.1324.52303
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 432 -
Rwork0.22 8337 -
obs--93.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9729-0.17120.01652.36610.0290.71850.0020.04280.00510.0888-0.0117-0.006-0.0378-0.01310.00960.01620.0240.0096-0.01260.017-0.1051139.753513.95048.2292
28.27982.1287-6.13291.3516-2.25595.68070.9977-1.07780.96120.5582-0.31160.5327-0.86590.5553-0.68610.3044-0.14470.27030.2302-0.18160.2609114.018427.796331.667
31.94110.0277-0.80061.9863-0.92162.8692-0.0681-0.1709-0.02690.17040.11790.12760.0177-0.1337-0.04980.04150.02660.03740.00130.0424-0.0123132.0136-5.997216.4309
49.77023.6494-1.62476.0606-1.01131.3012-0.02440.7045-0.2871-0.13870.16770.2531-0.3529-0.1179-0.14330.11010.02090.09180.1414-0.0520.1853107.897316.089723.2586
52.3570.46460.79480.96050.76273.126-0.0594-0.0302-0.08110.030.1243-0.0782-0.12080.1802-0.06490.0197-0.0083-0.0572-0.0337-0.0057-0.101968.871818.259423.1726
66.85282.07640.49476.69151.71251.1692-0.07270.3078-0.5622-0.25840.47-0.88020.1614-0.0797-0.39730.0982-0.00450.00110.1394-0.1820.409795.3803-3.690124.8287
71.2804-0.2481-0.07632.88320.13750.35070.0375-0.0787-0.13420.1536-0.0048-0.1740.04820.0298-0.0328-0.021-0.0088-0.0293-0.01450.004-0.07560.4794-2.86517.6525
86.70640.30223.5061.42150.53953.1438-0.0262-0.756-0.13370.33860.3203-0.21060.1340.0284-0.29410.14830.1001-0.16730.2435-0.10640.252990.8495-14.838535.2925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 1041 - 109
2X-RAY DIFFRACTION2AC105 - 213110 - 218
3X-RAY DIFFRACTION3BD1 - 1131 - 114
4X-RAY DIFFRACTION4BD114 - 227115 - 213
5X-RAY DIFFRACTION5HB1 - 1131 - 114
6X-RAY DIFFRACTION6HB114 - 227115 - 213
7X-RAY DIFFRACTION7LA1 - 1071 - 112
8X-RAY DIFFRACTION8LA108 - 213113 - 218

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