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- PDB-3cfd: Purple-fluorescent antibody EP2-25C10 in complex with its stilben... -

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Basic information

Entry
Database: PDB / ID: 3cfd
TitlePurple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten
Components
  • PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
  • PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / PURPLE-FLUORESCENT ANTIBODY / HAPTEN COMPLEX
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: 2.5 Å
AuthorsDebler, E.W. / Heine, A. / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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 9, 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: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
H: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
A: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
B: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5337
Polymers94,8234
Non-polymers7113
Water2,360131
1
A: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
B: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7213
Polymers47,4112
Non-polymers3091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-24.7 kcal/mol
Surface area19720 Å2
MethodPISA
2
L: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
H: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8134
Polymers47,4112
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-24.2 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 72.480, 77.230
Angle α, β, γ (deg.)91.98, 106.11, 114.15
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12L
22A
13H
23B
14H
24B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYSLA1 - 1071 - 107
21ASPASPLYSLYSAC1 - 1071 - 107
12ARGARGGLUGLULA108 - 213108 - 213
22ARGARGGLUGLUAC108 - 213108 - 213
13GLUGLUSERSERHB1 - 1131 - 120
23GLUGLUSERSERBD1 - 1131 - 120
14ALAALAPROPROHB114 - 227121 - 219
24ALAALAPROPROBD114 - 227121 - 219

NCS ensembles :
ID
1
2
3
4

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Components

#1: Antibody PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN


Mass: 23605.916 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 PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN


Mass: 23805.355 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growpH: 4.5
Details: AMMONIUM SULFATE, LITHIUM SULFATE, 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: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2002 / Details: MONOCHROMATOR
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 37156 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 50.1 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.525 / % possible all: 97.4

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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 2NZS

2nzs
PDB Unreleased entry


Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 19.235 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.562 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1746 5 %RANDOM
Rwork0.211 ---
obs0.212 33487 100 %-
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: 33.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-1.28 Å20.03 Å2
2---2.56 Å2-2.53 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 52 131 6824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226861
X-RAY DIFFRACTIONr_bond_other_d0.0080.024550
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9579355
X-RAY DIFFRACTIONr_angle_other_deg1.0963.00311102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76824.161274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.361151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7511532
X-RAY DIFFRACTIONr_chiral_restr0.0750.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027643
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021373
X-RAY DIFFRACTIONr_nbd_refined0.1970.21029
X-RAY DIFFRACTIONr_nbd_other0.2130.24425
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23122
X-RAY DIFFRACTIONr_nbtor_other0.0870.23805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3930.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.55511
X-RAY DIFFRACTIONr_mcbond_other0.0921.51744
X-RAY DIFFRACTIONr_mcangle_it0.77827016
X-RAY DIFFRACTIONr_scbond_it1.19433183
X-RAY DIFFRACTIONr_scangle_it1.6284.52339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L627tight positional0.020.05
2H627tight positional0.070.05
3A704tight positional0.020.05
4B577tight positional0.020.05
1L745medium positional0.080.5
2H774medium positional0.250.5
3A921medium positional0.130.5
4B596medium positional0.030.5
1L627tight thermal0.060.5
2H627tight thermal0.210.5
3A704tight thermal0.10.5
4B577tight thermal0.460.5
1L745medium thermal0.132
2H774medium thermal0.262
3A921medium thermal0.152
4B596medium thermal0.412
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 107 -
Rwork0.316 1940 -
obs--100 %
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)
12.993-1.0232-0.42882.06040.60712.1341-0.0774-0.1620.11090.1492-0.03670.2049-0.0005-0.13020.1142-0.1304-0.0274-0.0162-0.1052-0.0045-0.1699-12.6929-16.565548.9553
22.37342.418-0.07967.09020.07051.5512-0.00610.0771-0.0683-0.0189-0.0919-0.1361-0.13630.02560.0981-0.02670.1085-0.0432-0.04920.0288-0.1086-11.303619.618158.6947
33.10090.68530.14294.39160.50141.61790.0069-0.0320.15980.03580.1312-0.0546-0.08120.0711-0.1381-0.17560.028-0.0101-0.1599-0.0103-0.17159.4418-15.517250.2843
44.89810.6657-1.67283.45591.75083.89060.0817-0.34470.1270.25920.0179-0.2285-0.04450.1241-0.09960.05490.1304-0.0832-0.04770.0568-0.0527-0.827112.952568.0523
52.47151.07630.47942.62660.92512.1242-0.07040.2449-0.1566-0.20540.05790.25140.0031-0.13210.0124-0.13430.0141-0.0071-0.10310.0164-0.1438-12.288434.259727.0876
61.8802-2.13450.64179.67050.95310.9434-0.00680.0634-0.0275-0.0925-0.0439-0.4440.1309-0.04220.0507-0.0047-0.11630.1027-0.015-0.0001-0.0652-11.1027-2.04917.4567
73.6179-0.0693-0.81183.64680.58022.1218-0.0771-0.026-0.2931-0.13870.1473-0.02050.12990.1161-0.0702-0.1489-0.02860.011-0.1655-0.0079-0.18939.858633.127925.901
86.24410.49290.91763.51021.3443.7389-0.16140.7515-0.1501-0.34570.2031-0.45550.07850.1008-0.04170.0927-0.14470.21260.0171-0.03160.2241-0.2094.38398.2234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1071 - 107
2X-RAY DIFFRACTION2LA108 - 213108 - 213
3X-RAY DIFFRACTION3HB1 - 1131 - 120
4X-RAY DIFFRACTION4HB114 - 228121 - 220
5X-RAY DIFFRACTION5AC1 - 1071 - 107
6X-RAY DIFFRACTION6AC108 - 213108 - 213
7X-RAY DIFFRACTION7BD1 - 1131 - 120
8X-RAY DIFFRACTION8BD114 - 227121 - 219

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