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

ID or keywords:

Entry

Database: PDB / ID: 3cfd

Title

Purple-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

Keywords

IMMUNE SYSTEM / IMMUNOGLOBULIN / PURPLE-FLUORESCENT ANTIBODY / HAPTEN COMPLEX

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Debler, E.W. / Heine, A. / Wilson, I.A.

Citation

Journal: 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

Deposition	Mar 3, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3cfd.cif.gz	178.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3cfd.ent.gz	141.2 KB	Display	PDB format
PDBx/mmJSON format	3cfd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3cfd_validation.pdf.gz	929.7 KB	Display	wwPDB validaton report
Full document	3cfd_full_validation.pdf.gz	942.3 KB	Display
Data in XML	3cfd_validation.xml.gz	33 KB	Display
Data in CIF	3cfd_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/3cfd ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cfd	HTTPS FTP

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Related structure data

Related structure data	3cfbC 3cfcC 3cfeC 2nzs PDB Unreleased entryS 1fl3 1ub5 1ub6 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5waw-d 3cfe-2 5i1l-2 6m87-2 6c6x-3 4m7z-1 3ls5-d 6p9i-1 5lgh-d 3cmo-1 4odv-d 1dbb-d 5ywf-1 2fjf-8 5ocx-d 4h20-d 2fjf-5 3e8u-d 6al4-3 2ai0-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

3cfbC

3cfcC

3cfeC

2nzs
PDB Unreleased entryS

1fl3

1ub5

1ub6

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

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

95.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN

B: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN

hetero molecules

defined by author&software
47.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

L: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN

H: PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN

hetero molecules

defined by author&software
47.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	A
1	2	L
2	2	A
1	3	H
2	3	B
1	4	H
2	4	B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	LYS	LYS	L	A	1 - 107	1 - 107
2	1	ASP	ASP	LYS	LYS	A	C	1 - 107	1 - 107
1	2	ARG	ARG	GLU	GLU	L	A	108 - 213	108 - 213
2	2	ARG	ARG	GLU	GLU	A	C	108 - 213	108 - 213
1	3	GLU	GLU	SER	SER	H	B	1 - 113	1 - 120
2	3	GLU	GLU	SER	SER	B	D	1 - 113	1 - 120
1	4	ALA	ALA	PRO	PRO	H	B	114 - 227	121 - 219
2	4	ALA	ALA	PRO	PRO	B	D	114 - 227	121 - 219

NCS ensembles :

ID
1
2
3
4

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.78 %
Crystal grow	pH: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2002 / Details: MONOCHROMATOR
Radiation	Monochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 37156 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / B_iso Wilson estimate: 50.1 Å² / R_sym value: 0.083 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / R_sym value: 0.525 / % possible all: 97.4

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.3.0017	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NZS

2nzs
PDB Unreleased entry

Resolution: 2.5→29.88 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.243	1746	5 %	RANDOM
R_work	0.211	-	-	-
obs	0.212	33487	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 33.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.48 Å²	-1.28 Å²	0.03 Å²
2-	-	-2.56 Å²	-2.53 Å²
3-	-	-	1.84 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6641	0	52	131	6824

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	6861
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	4550
X-RAY DIFFRACTION	r_angle_refined_deg	1.304	1.957	9355
X-RAY DIFFRACTION	r_angle_other_deg	1.096	3.003	11102
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.43	5	861
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.768	24.161	274
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.361	15	1079
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.751	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1051
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7643
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1373
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	1029
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	4425
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3122
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	3805
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	161
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.255	0.2	27
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.393	0.2	70
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.066	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.746	1.5	5511
X-RAY DIFFRACTION	r_mcbond_other	0.092	1.5	1744
X-RAY DIFFRACTION	r_mcangle_it	0.778	2	7016
X-RAY DIFFRACTION	r_scbond_it	1.194	3	3183
X-RAY DIFFRACTION	r_scangle_it	1.628	4.5	2339
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	L	627	tight positional	0.02	0.05
2	H	627	tight positional	0.07	0.05
3	A	704	tight positional	0.02	0.05
4	B	577	tight positional	0.02	0.05
1	L	745	medium positional	0.08	0.5
2	H	774	medium positional	0.25	0.5
3	A	921	medium positional	0.13	0.5
4	B	596	medium positional	0.03	0.5
1	L	627	tight thermal	0.06	0.5
2	H	627	tight thermal	0.21	0.5
3	A	704	tight thermal	0.1	0.5
4	B	577	tight thermal	0.46	0.5
1	L	745	medium thermal	0.13	2
2	H	774	medium thermal	0.26	2
3	A	921	medium thermal	0.15	2
4	B	596	medium thermal	0.41	2

LS refinement shell

Resolution: 2.5→2.56 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.349	107	-
R_work	0.316	1940	-
obs	-	-	100 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.993	-1.0232	-0.4288	2.0604	0.6071	2.1341	-0.0774	-0.162	0.1109	0.1492	-0.0367	0.2049	-0.0005	-0.1302	0.1142	-0.1304	-0.0274	-0.0162	-0.1052	-0.0045	-0.1699	-12.6929	-16.5655	48.9553
2	2.3734	2.418	-0.0796	7.0902	0.0705	1.5512	-0.0061	0.0771	-0.0683	-0.0189	-0.0919	-0.1361	-0.1363	0.0256	0.0981	-0.0267	0.1085	-0.0432	-0.0492	0.0288	-0.1086	-11.3036	19.6181	58.6947
3	3.1009	0.6853	0.1429	4.3916	0.5014	1.6179	0.0069	-0.032	0.1598	0.0358	0.1312	-0.0546	-0.0812	0.0711	-0.1381	-0.1756	0.028	-0.0101	-0.1599	-0.0103	-0.1715	9.4418	-15.5172	50.2843
4	4.8981	0.6657	-1.6728	3.4559	1.7508	3.8906	0.0817	-0.3447	0.127	0.2592	0.0179	-0.2285	-0.0445	0.1241	-0.0996	0.0549	0.1304	-0.0832	-0.0477	0.0568	-0.0527	-0.8271	12.9525	68.0523
5	2.4715	1.0763	0.4794	2.6266	0.9251	2.1242	-0.0704	0.2449	-0.1566	-0.2054	0.0579	0.2514	0.0031	-0.1321	0.0124	-0.1343	0.0141	-0.0071	-0.1031	0.0164	-0.1438	-12.2884	34.2597	27.0876
6	1.8802	-2.1345	0.6417	9.6705	0.9531	0.9434	-0.0068	0.0634	-0.0275	-0.0925	-0.0439	-0.444	0.1309	-0.0422	0.0507	-0.0047	-0.1163	0.1027	-0.015	-0.0001	-0.0652	-11.1027	-2.049	17.4567
7	3.6179	-0.0693	-0.8118	3.6468	0.5802	2.1218	-0.0771	-0.026	-0.2931	-0.1387	0.1473	-0.0205	0.1299	0.1161	-0.0702	-0.1489	-0.0286	0.011	-0.1655	-0.0079	-0.1893	9.8586	33.1279	25.901
8	6.2441	0.4929	0.9176	3.5102	1.344	3.7389	-0.1614	0.7515	-0.1501	-0.3457	0.2031	-0.4555	0.0785	0.1008	-0.0417	0.0927	-0.1447	0.2126	0.0171	-0.0316	0.2241	-0.209	4.3839	8.2234

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	L	A	1 - 107	1 - 107
2	X-RAY DIFFRACTION	2	L	A	108 - 213	108 - 213
3	X-RAY DIFFRACTION	3	H	B	1 - 113	1 - 120
4	X-RAY DIFFRACTION	4	H	B	114 - 228	121 - 220
5	X-RAY DIFFRACTION	5	A	C	1 - 107	1 - 107
6	X-RAY DIFFRACTION	6	A	C	108 - 213	108 - 213
7	X-RAY DIFFRACTION	7	B	D	1 - 113	1 - 120
8	X-RAY DIFFRACTION	8	B	D	114 - 227	121 - 219

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