PDB-3cfe: Crystal structure of purple-fluorescent antibody EP2-25C10

ID or keywords:

Entry

Database: PDB / ID: 3cfe

Title

Crystal structure of purple-fluorescent antibody EP2-25C10

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

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / PHASER / Resolution: 2.99 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	3cfe.cif.gz	174.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3cfe.ent.gz	138.9 KB	Display	PDB format
PDBx/mmJSON format	3cfe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3cfe_validation.pdf.gz	478.4 KB	Display	wwPDB validaton report
Full document	3cfe_full_validation.pdf.gz	492.6 KB	Display
Data in XML	3cfe_validation.xml.gz	31.3 KB	Display
Data in CIF	3cfe_validation.cif.gz	42.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/3cfe ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cfe	HTTPS FTP

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Related structure data

Related structure data	3cfbC 3cfcC 3cfdC 3hfmS 1fl3 1ub5 1ub6 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ye4-2 4kjq-2 3wii-1 4wht-8 6y54-1 6ug9-2 4j8r-2 5yfi-d 6wrp-d 4ncc-2 5tr8-d 2g2r-2 2fjf-6 4d9l-1 1mex-d 4kk5-2 6wos-d 4mhh-3 7jwp-1 6c6x-4 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

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

95.6 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
47.8 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)	132.130, 59.460, 149.370
Angle α, β, γ (deg.)	90.00, 100.37, 90.00
Int Tables number	5
Space group name H-M	C121

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	VAL	VAL	SER	SER	H	B	2 - 113	2 - 120
2	3	VAL	VAL	SER	SER	B	D	2 - 113	2 - 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
Sequence details	THE SEQUENCES OF THE FAB COMPLEXES ARE NOT AVAILABLE IN ANY SEQUENCE DATABASES.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.57 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.972386
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2002 / Details: FLAT MIRROR (VERTICAL FOCUSING)
Radiation	Monochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.972386 Å / Relative weight: 1
Reflection	Resolution: 2.99→25 Å / Num. obs: 20613 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / B_iso Wilson estimate: 58.5 Å² / R_sym value: 0.112 / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.99→3.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.6 / R_sym value: 0.479 / % possible all: 89.5

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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: PHASER
Starting model: PDB ENTRY 3HFM

3hfm

Resolution: 2.99→24.46 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.899 / SU B: 41.913 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.255	960	4.8 %	RANDOM
R_work	0.211	-	-	-
obs	0.213	18943	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: 18.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.65 Å²	0 Å²	-1.97 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	1.96 Å²

Refinement step

Cycle: LAST / Resolution: 2.99→24.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6634	0	43	0	6677

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6835
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4524
X-RAY DIFFRACTION	r_angle_refined_deg	1.481	1.954	9323
X-RAY DIFFRACTION	r_angle_other_deg	0.911	3.003	11046
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.131	5	860
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.735	24.161	274
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.637	15	1078
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.498	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1050
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7580
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1346
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1282
X-RAY DIFFRACTION	r_nbd_other	0.214	0.2	4553
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	3288
X-RAY DIFFRACTION	r_nbtor_other	0.093	0.2	4026
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	206
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.089	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.278	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.28	0.2	55
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.313	0.2	4
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	0.359	1.5	5405
X-RAY DIFFRACTION	r_mcbond_other	0.085	1.5	1742
X-RAY DIFFRACTION	r_mcangle_it	0.5	2	7004
X-RAY DIFFRACTION	r_scbond_it	0.881	3	3031
X-RAY DIFFRACTION	r_scangle_it	1.322	4.5	2319
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	1372	tight positional	0.03	0.05
2	L	1401	tight positional	0.03	0.05
3	H	1611	tight positional	0.03	0.05
4	H	1173	tight positional	0.03	0.05
1	L	1372	tight thermal	0.07	0.5
2	L	1401	tight thermal	0.06	0.5
3	H	1611	tight thermal	0.08	0.5
4	H	1173	tight thermal	0.08	0.5

LS refinement shell

Resolution: 2.99→3.07 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.423	55	-
R_work	0.346	1201	-
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	2.4974	-2.949	3.0758	8.0568	-4.5855	4.9039	-0.1184	0.016	-0.0373	0.5341	0.0565	-0.0278	-0.9475	-0.0626	0.0619	0.2462	-0.0543	0.0227	0.1059	-0.0143	0.1499	-6.2286	50.3078	139.8862
2	0.8351	-0.9522	0.3889	1.8798	-0.0322	0.394	-0.0745	0.1928	0.2298	-0.2098	-0.0634	-0.0506	-0.2059	0.0445	0.1379	0.1702	-0.069	0.0171	0.1441	0.0162	0.0724	0.163	44.9838	135.5471
3	7.061	3.4014	0.4383	2.8273	0.1157	0.4005	-0.0471	-0.0837	-0.1585	0.1528	0.0485	-0.0305	-0.0484	0.0128	-0.0013	0.2821	0.077	0.0193	0.1945	0.0076	0.0568	-33.2904	44.9332	126.3564
4	26.8106	5.0192	3.8146	23.4357	-2.5392	1.0132	0.2202	-0.7424	-1.3242	-0.0211	-0.5063	0.4567	-0.0678	-0.7894	0.2861	0.1901	0.0026	0.0506	0.3492	-0.0759	-0.0393	-50.7319	37.7878	126.6932
5	11.4299	9.2089	1.1701	8.1439	2.3172	2.728	0.1284	-0.3316	0.3649	0.0302	-0.3362	0.3605	-0.4012	-0.4102	0.2078	0.257	0.1509	-0.0378	0.2875	0.0289	0.3621	-41.3247	52.1347	124.8146
6	31.7498	22.6696	-11.1262	27.4427	-16.45	10.3264	-0.0636	1.5947	1.0078	-1.7232	0.6674	0.9949	0.8254	0.0616	-0.6038	0.3386	0.1098	-0.0249	0.1274	-0.1031	0.0673	-2.4634	26.3388	123.3979
7	4.5187	-0.7922	-0.2263	2.7064	-0.0266	1.8966	0.0697	-0.0233	-0.0945	0.1238	0.0044	0.0201	-0.028	-0.0741	-0.0741	0.1641	-0.0059	-0.0395	0.0612	0.0059	0.0194	-1.3388	24.1474	135.371
8	4.1049	0.9465	2.753	0.2183	0.6348	1.8464	-0.3134	0.4282	-0.365	0.2155	0.205	0.1627	-0.2656	-0.0718	0.1085	0.2235	-0.018	-0.0527	0.1697	0.0078	0.31	-23.3352	26.3897	126.5147
9	5.1073	-0.6352	2.4914	12.6326	-6.2735	5.2856	-0.0426	0.0821	0.3699	-0.406	0.1121	0.0959	-0.1603	-0.3515	-0.0695	0.3165	0.0422	0.0619	0.3845	-0.1223	-0.0125	-33.244	37.3865	118.4665
10	4.5609	-0.6562	2.2024	5.129	-1.748	2.573	-0.0398	0.455	-0.157	-0.6517	-0.1456	-0.2962	0.2752	0.2996	0.1854	0.1926	0.0224	0.0869	0.2535	-0.0541	0.1699	-28.8466	35.1697	114.9749
11	54.5945	34.3564	-15.7988	28.2916	-7.3509	5.5785	0.5843	0.6901	0.8834	-0.9598	0.0122	0.4227	-0.552	0.1402	-0.5964	0.2499	0.0961	-0.0711	0.1318	0.1284	0.2175	10.7695	-12.5014	50.2485
12	4.5145	-0.6393	-0.0097	3.1916	0.3422	1.6716	0.0487	0.077	-0.1275	0.0683	-0.0185	0.1331	0.0329	-0.0192	-0.0302	0.0348	0.0061	0.0058	0.0805	0.0049	-0.0008	12.0403	-14.0834	62.0708
13	4.7902	-1.9107	0.8586	1.73	-0.5925	0.2185	0.507	0.521	-1.6441	-0.1692	-0.3561	0.7653	0.0041	-0.0777	-0.1509	0.1266	0.091	-0.0541	0.2023	-0.1837	0.4899	-12.1994	-12.9756	53.2885
14	7.1979	0.1759	1.1877	9.0492	-5.7022	5.7699	0.2184	0.3857	-0.8328	-0.8735	0.3068	0.2511	0.0184	-0.2944	-0.5252	0.3287	0.1012	-0.0078	0.2411	-0.249	0.3225	-20.2316	-1.5482	45.3752
15	3.3696	0.5764	1.8044	8.1267	-1.7883	3.2316	0.0654	0.6898	-0.3353	-1.0354	-0.1893	-0.512	0.2117	-0.2621	0.1239	0.2073	0.1919	0.0524	0.4473	-0.2068	0.3788	-15.9705	-3.9018	41.8195
16	3.9539	-0.9062	1.1649	6.7489	-3.3383	4.548	0.0111	-0.437	0.4263	0.5815	-0.1538	0.0319	-0.9504	-0.1327	0.1427	0.0888	0.0211	0.0236	0.1081	-0.0809	0.2104	7.1476	11.9659	66.1025
17	2.22	-0.505	0.3029	2.2774	-0.0148	1.5069	-0.0031	0.2484	0.3209	-0.2488	-0.0228	-0.124	-0.1275	0.0596	0.0259	0.0457	-0.0163	0.0305	0.0973	-0.0249	0.0941	13.5395	6.5834	61.8287
18	7.8611	1.8684	0.806	3.2078	-0.0867	0.1107	0.145	0.107	-0.4613	0.1827	-0.1109	-0.1131	0.0178	0.071	-0.0341	0.1973	0.1233	-0.0435	0.1864	-0.0339	0.1731	-20.0248	6.2636	53.0197
19	1.1905	0.7998	-1.494	5.8506	4.3712	7.3125	0.0157	-0.3072	-1.438	0.1992	-0.1793	-0.3063	0.5945	-0.8391	0.1636	0.1637	0.1082	-0.0941	0.3226	-0.0128	0.5034	-37.5026	-0.7916	53.8424
20	6.7112	4.357	1.2882	7.882	0.5268	2.4194	0.5292	0.0917	0.3788	0.3916	-0.5981	0.0524	0.1218	-0.2023	0.0689	0.1252	0.1351	0.0829	0.3582	-0.027	0.1012	-28.0456	13.4411	51.3766

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	A	C	1 - 24	1 - 24
2	X-RAY DIFFRACTION	2	A	C	25 - 105	25 - 105
3	X-RAY DIFFRACTION	3	A	C	106 - 182	106 - 182
4	X-RAY DIFFRACTION	4	A	C	183 - 193	183 - 193
5	X-RAY DIFFRACTION	5	A	C	194 - 213	194 - 213
6	X-RAY DIFFRACTION	6	B	D	1 - 9	1 - 9
7	X-RAY DIFFRACTION	7	B	D	10 - 102	10 - 109
8	X-RAY DIFFRACTION	8	B	D	103 - 125	110 - 132
9	X-RAY DIFFRACTION	9	B	D	126 - 152	133 - 157
10	X-RAY DIFFRACTION	10	B	D	153 - 227	158 - 219
11	X-RAY DIFFRACTION	11	H	B	1 - 9	1 - 9
12	X-RAY DIFFRACTION	12	H	B	10 - 103	10 - 110
13	X-RAY DIFFRACTION	13	H	B	104 - 125	111 - 132
14	X-RAY DIFFRACTION	14	H	B	126 - 152	133 - 157
15	X-RAY DIFFRACTION	15	H	B	153 - 227	158 - 219
16	X-RAY DIFFRACTION	16	L	A	1 - 24	1 - 24
17	X-RAY DIFFRACTION	17	L	A	25 - 105	25 - 105
18	X-RAY DIFFRACTION	18	L	A	106 - 182	106 - 182
19	X-RAY DIFFRACTION	19	L	A	183 - 193	183 - 193
20	X-RAY DIFFRACTION	20	L	A	194 - 213	194 - 213

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