PDB-1vcl: Crystal Structure of Hemolytic Lectin CEL-III

ID or keywords:

Entry

Database: PDB / ID: 1vcl

Title

Crystal Structure of Hemolytic Lectin CEL-III

Components

hemolytic lectin CEL-III

Keywords

TOXIN /

LECTIN / CEL-III /

HEMOLYSIS /

HEMAGGLUTINATION / PORE-FORMING /

CALCIUM

Function / homology

Function and homology information

positive regulation of erythrocyte aggregation /

melibiose binding /

lactose binding / cell killing /

N-acetylgalactosamine binding /

fucose binding / disruption of plasma membrane integrity in another organism /

galactose binding /

hemolysis in another organism / protein homooligomerization ...
Similarity search - Function

Biological species

Cucumaria echinata (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.7 Å

Authors

Uchida, T. / Yamasaki, T. / Eto, S. / Sugawara, H. / Kurisu, G. / Nakagawa, A. / Kusunoki, M. / Hatakeyama, T.

Citation

Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Hemolytic Lectin CEL-III Isolated from the Marine Invertebrate Cucumaria echinata: IMPLICATIONS OF DOMAIN STRUCTURE FOR ITS MEMBRANE PORE-FORMATION MECHANISM
Authors: Uchida, T. / Yamasaki, T. / Eto, S. / Sugawara, H. / Kurisu, G. / Nakagawa, A. / Kusunoki, M. / Hatakeyama, T.

History

Deposition	Mar 9, 2004	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 7, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 2.0	Dec 25, 2019	Group: Database references / Derived calculations / Polymer sequence Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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	1vcl.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb1vcl.ent.gz	277.5 KB	Display	PDB format
PDBx/mmJSON format	1vcl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vc/1vcl ftp://data.pdbj.org/pub/pdb/validation_reports/vc/1vcl	HTTPS FTP

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Related structure data

Similar structure data	2z48-2 2z48-1 2z49-2 1exc-2 7ksj-d 3hi2-d 3fi2-d 4oo0-d 3ax2-d 2z49-1 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#161 - May 2013 Ricin similarity (5) #69 - Sep 2005 Cholera Toxin similarity (5)

Deposited unit

A: hemolytic lectin CEL-III

B: hemolytic lectin CEL-III

hetero molecules

95.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: hemolytic lectin CEL-III

hetero molecules

defined by author
47.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: hemolytic lectin CEL-III

hetero molecules

defined by author
47.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.42, 65.37, 126.02
Angle α, β, γ (deg.)	90.00, 98.18, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	hemolytic lectin CEL-III Mass: 47452.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q868M7

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Non-polymers , 5 types, 863 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 846 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 38.48 %

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→26.2 Å / Num. all: 92828 / Num. obs: 92828
Reflection shell	Resolution: 1.7→1.79 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.7→26.17 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.952 / SU B: 2.034 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20116	4642	5 %	RANDOM
R_work	0.16519	-	-	-
all	0.167	-	-	-
obs	0.167	88165	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 13.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0 Å²	0.64 Å²
2-	-	0.64 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→26.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6626	0	30	846	7502

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.021	6785
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	5708
X-RAY DIFFRACTION	r_angle_refined_deg	1.365	1.943	9218
X-RAY DIFFRACTION	r_angle_other_deg	0.79	3	13369
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.58	5	862
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	995
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7766
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1342
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	1330
X-RAY DIFFRACTION	r_nbd_other	0.252	0.2	7041
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	3954
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	632
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.215	0.2	52
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.085	0.2	14
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.331	0.2	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.165	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.837	1.5	4265
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.485	2	6869
X-RAY DIFFRACTION	r_scbond_it	2.006	3	2520
X-RAY DIFFRACTION	r_scangle_it	3.215	4.5	2349
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.218	306
R_work	0.184	6540

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	0.7174	-0.4801	-1.02	1.7296	0.5894	2.0715	0.0075	-0.3505	0.2803	0.05	0.2755	-0.4062	0.0216	0.233	-0.283	0.1272	-0.0247	-0.0226	0.2718	-0.1498	0.2087	12.374	46.418	22.382
2	2.168	-1.6187	-0.6937	2.5196	-0.0777	2.34	0.0286	-0.5985	0.5007	0.0404	0.3472	-0.3328	-0.3398	-0.0258	-0.3758	0.2058	-0.0151	0.0425	0.2276	-0.1867	0.2078	0.584	57.924	26.533
3	2.6618	-1.6704	-0.0669	2.0932	0.2833	1.0441	0.2936	0.0253	0.6524	-0.2887	-0.0287	-0.4784	-0.322	0.1151	-0.2649	0.3103	-0.0726	0.1715	0.0451	-0.0366	0.3425	10.497	59.036	11.076
4	2.8682	-0.0763	0.0845	2.4205	0.7349	0.6174	-0.2562	-0.7414	0.0161	0.3664	0.2177	-0.0314	0.2329	0.0824	0.0385	0.2396	0.115	-0.0095	0.3164	0.0378	0.0729	16.476	18.857	20.019
5	1.2383	-0.7218	-0.7979	0.8872	0.2163	1.2295	-0.0734	-0.2505	0.2681	-0.0346	0.1774	-0.2478	-0.002	0.1251	-0.104	0.1187	-0.0079	-0.0147	0.201	-0.0803	0.201	20.701	30.633	9.015
6	0.6645	0.0989	-0.4764	1.6334	0.0511	2.271	-0.1456	-0.0567	-0.0116	0.0014	0.1809	-0.2178	0.333	0.2294	-0.0353	0.1924	0.0666	-0.0213	0.1709	-0.0261	0.1528	22.295	14.174	4.878
7	2.7707	-0.7476	-2.0788	0.5726	0.6223	1.1286	-0.3072	-0.1549	-0.4388	0.0784	-0.0208	0.2343	0.0096	0.2288	0.328	0.1096	0.0106	0.0291	0.185	0.0278	0.2129	-4.935	29.822	16.908
8	2.88	-0.7936	-1.2003	0.6894	0.5623	0.6131	-0.0535	-0.3308	-0.1544	0.0733	-0.1162	0.1487	0.0294	0.0679	0.1697	0.135	-0.0289	0.0209	0.2301	-0.0184	0.1106	-16.043	37.245	22.011
9	2.0321	-0.8653	-0.8696	1.4782	-0.164	1.1633	0.1195	0.5993	0.3191	-0.134	0.0448	0.306	0.0504	-0.2798	-0.1643	0.1159	0.0092	-0.0566	0.3167	0.1599	0.2404	4.97	74.684	40.115
10	3.1617	-0.9259	-0.9003	3.2109	0.2419	2.1979	0.5049	0.802	0.9299	-0.4831	-0.1086	-0.4065	-0.2903	-0.1852	-0.3962	0.2317	0.1158	0.1492	0.2396	0.2861	0.3423	16.785	85.883	35.454
11	2.5843	0.7646	-0.6353	2.606	-1.0419	1.8201	0.2043	0.0083	0.7676	0.0689	0.1354	0.2414	-0.1325	-0.2682	-0.3397	0.1305	0.0511	0.0665	0.0651	0.075	0.473	7.125	87.458	51.125
12	2.066	-0.2027	-0.1689	1.6319	-0.9664	1.1745	-0.1532	0.6106	-0.1249	-0.1271	0.115	0.052	0.1334	-0.0793	0.0382	0.1674	-0.0871	-0.011	0.2808	-0.0508	0.1154	0.697	47.401	42.918
13	2.3299	0.5687	-0.3504	0.5016	-0.0599	0.5879	-0.1441	0.2157	0.2202	-0.0019	0.1416	0.1514	-0.0417	-0.0637	0.0026	0.1258	-0.0171	-0.0417	0.211	0.0686	0.1731	-3.409	59.141	53.839
14	1.7158	0.0628	-0.0017	1.4966	-0.1336	1.0716	-0.1664	0.0184	-0.1861	-0.0528	0.1564	0.1601	0.1405	-0.1588	0.01	0.1548	-0.0422	-0.0047	0.157	0.0368	0.1992	-5.2	42.685	58.023
15	2.3691	0.1695	-1.1425	0.041	0.3254	1.1298	-0.1395	0.1078	-0.0749	0.0211	-0.0602	-0.069	0.0384	-0.1379	0.1997	0.123	-0.0321	-0.0144	0.1901	0.0047	0.1594	22.207	57.598	46.001
16	1.7148	0.5845	-0.3289	0.3367	-0.2373	0.2615	-0.0967	0.1885	0.0474	-0.0857	0.0276	-0.0741	0.028	-0.0121	0.0691	0.1735	-0.0356	0.0121	0.1722	-0.0057	0.1197	33.23	64.794	40.306

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	A	12 - 48	12 - 48
2	X-RAY DIFFRACTION	1	A	C	1001
3	X-RAY DIFFRACTION	1	A	H	1101
4	X-RAY DIFFRACTION	2	A	A	53 - 79	53 - 79
5	X-RAY DIFFRACTION	2	A	A	85 - 92	85 - 92
6	X-RAY DIFFRACTION	3	A	A	110 - 146	110 - 146
7	X-RAY DIFFRACTION	3	A	D	1002
8	X-RAY DIFFRACTION	4	A	A	157 - 193	157 - 193
9	X-RAY DIFFRACTION	4	A	E	1003
10	X-RAY DIFFRACTION	4	A	I	1102
11	X-RAY DIFFRACTION	5	A	A	198 - 234	198 - 234
12	X-RAY DIFFRACTION	5	A	F	1004	1
13	X-RAY DIFFRACTION	5	A	Q - A	1201	1
14	X-RAY DIFFRACTION	6	A	A	245 - 281	245 - 281
15	X-RAY DIFFRACTION	6	A	G	1005	1
16	X-RAY DIFFRACTION	7	A	A	320 - 354	320 - 354
17	X-RAY DIFFRACTION	8	A	A	284 - 319	284 - 319
18	X-RAY DIFFRACTION	8	A	A	355 - 432	355 - 432
19	X-RAY DIFFRACTION	9	B	B	12 - 48	12 - 48
20	X-RAY DIFFRACTION	9	B	J	1001	1
21	X-RAY DIFFRACTION	9	B	O	1101	1
22	X-RAY DIFFRACTION	10	B	B	53 - 79	53 - 79
23	X-RAY DIFFRACTION	10	B	B	85 - 92	85 - 92
24	X-RAY DIFFRACTION	11	B	B	110 - 146	110 - 146
25	X-RAY DIFFRACTION	11	B	K	1002	1
26	X-RAY DIFFRACTION	12	B	B	157 - 193	157 - 193
27	X-RAY DIFFRACTION	12	B	L	1003	1
28	X-RAY DIFFRACTION	12	B	P	1102	1
29	X-RAY DIFFRACTION	13	B	B	198 - 234	198 - 234
30	X-RAY DIFFRACTION	13	B	M	1004	1
31	X-RAY DIFFRACTION	13	B	R	2201	1
32	X-RAY DIFFRACTION	14	B	B	245 - 281	245 - 281
33	X-RAY DIFFRACTION	14	B	N	1005	1
34	X-RAY DIFFRACTION	15	B	B	320 - 354	320 - 354
35	X-RAY DIFFRACTION	16	B	B	284 - 319	284 - 319
36	X-RAY DIFFRACTION	16	B	B	355 - 432	355 - 432

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 863 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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