PDB-2j3z: Crystal structure of the enzymatic component C2-I of the C2-toxin...

ID or keywords:

Entry

Database: PDB / ID: 2j3z

Title

Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1

Components

C2 TOXIN COMPONENT I

Keywords

TOXIN /

ADP-RIBOSYLTRANSFERASE /

CLOSTRIDIUM BOTULINUM

Function / homology

Function and homology information

extracellular region
Similarity search - Function

Biological species

CLOSTRIDIUM BOTULINUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E.

Citation

Journal: J.Mol.Biol. / Year: 2006
Title: Structure and Action of the Binary C2 Toxin from Clostridium Botulinum.
Authors: Schleberger, C. / Hochmann, H. / Barth, H. / Aktories, K. / Schulz, G.E.

History

Deposition	Aug 23, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 11, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_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.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2j3z.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3z ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3z	HTTPS FTP

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Related structure data

Related structure data	2j3vSC 2j3xC 2j42C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5eqa-2 5eq9-2 3ii1-d 5gqc-1 3fw6-d 5gqg-2 6w5x-d 2j3x-d 1i4h-d 6ptz-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2j3vSC

2j3xC

2j42C

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: C2 TOXIN COMPONENT I

B: C2 TOXIN COMPONENT I

C: C2 TOXIN COMPONENT I

D: C2 TOXIN COMPONENT I

E: C2 TOXIN COMPONENT I

F: C2 TOXIN COMPONENT I

hetero molecules

302 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: C2 TOXIN COMPONENT I

hetero molecules

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

2

B: C2 TOXIN COMPONENT I

hetero molecules

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

3

C: C2 TOXIN COMPONENT I

hetero molecules

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

4

D: C2 TOXIN COMPONENT I

hetero molecules

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

5

E: C2 TOXIN COMPONENT I

hetero molecules

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

6

F: C2 TOXIN COMPONENT I

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.421, 272.898, 246.290
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C
1	3	D
2	3	E
3	3	F
1	4	D
2	4	E
3	4	F

NCS domain segments:

Component-ID: 1 / Refine code: 4

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	PHE	PHE	PHE	PHE	A	A	10 - 221	10 - 221
2	1	PHE	PHE	PHE	PHE	B	B	10 - 221	10 - 221
3	1	PHE	PHE	PHE	PHE	C	C	10 - 221	10 - 221
1	2	TYR	TYR	VAL	VAL	A	A	222 - 420	222 - 420
2	2	TYR	TYR	VAL	VAL	B	B	222 - 420	222 - 420
3	2	TYR	TYR	VAL	VAL	C	C	222 - 420	222 - 420
1	3	PHE	PHE	PHE	PHE	D	D	10 - 221	10 - 221
2	3	PHE	PHE	PHE	PHE	E	E	10 - 221	10 - 221
3	3	PHE	PHE	PHE	PHE	F	F	10 - 221	10 - 221
1	4	TYR	TYR	VAL	VAL	D	D	222 - 420	222 - 420
2	4	TYR	TYR	VAL	VAL	E	E	222 - 420	222 - 420
3	4	TYR	TYR	VAL	VAL	F	F	222 - 420	222 - 420

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.999969, 0.007882, 0.000791), (0.003409, -0.518299, 0.855193), (0.00715, -0.855163, -0.518309)	-1.0429, 112.2725, 185.6765
2	given	(0.999966, -0.002033, -0.007963), (-0.007922, -0.495986, -0.868294), (-0.002184, 0.868328, -0.495986)	0.6703, 215.8952, -1.8538
3	given	(0.999958, -0.002249, 0.008904), (-0.008827, -0.502976, 0.864255), (0.002535, -0.864298, -0.502975)	-0.4305, 110.0379, 186.6458
4	given	(0.999365, -0.033918, -0.01088), (-0.025332, -0.462005, -0.886516), (0.025042, 0.886229, -0.462571)	3.8825, 215.4, -6.8478

#1: Protein	C2 TOXIN COMPONENT I / ADP-RIBOSYLTRANSFERASE C2-I Mass: 49391.684 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PET-3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O69275
#2: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN B, HIS 77 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN B, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN C, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN D, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN E, HIS 77 TO ARG ENGINEERED RESIDUE IN CHAIN F, HIS 77 TO ARG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.8 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6.1 Details: PROTEIN: 14 MG/ML IN H2O RESERVOIR: 0.1 M MES PH 6.1, 2.1 M (NH4)2SO4, 0.03 M COCL2 HANGING DROP 1:1

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813
Detector	Type: MARRESEARCH / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.813 Å / Relative weight: 1
Reflection	Resolution: 2.26→91 Å / Num. obs: 136331 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / R_merge(I) obs: 0.04 / Net I/σ(I): 23.7
Reflection shell	Resolution: 2.26→2.36 Å / R_merge(I) obs: 0.13 / Mean I/σ(I) obs: 8.8 / % possible all: 77.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J3V

2j3v

Resolution: 2.3→40 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.9 / SU B: 16.126 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	2650	2 %	RANDOM
R_work	0.2	-	-	-
obs	0.201	129810	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: 38.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.73 Å²	0 Å²	0 Å²
2-	-	-0.51 Å²	0 Å²
3-	-	-	-3.22 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20631	0	279	592	21502

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	21214
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.603	1.977	28623
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.343	5	2547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.818	25.367	1036
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.475	15	3968
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.429	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	3179
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	15682
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	9630
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	14431
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	1142
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	0.258	0.2	125
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.208	0.2	20
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	0.542	1.5	13170
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.899	2	20696
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.412	3	9110
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.194	4.5	7927
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1727	medium positional	0.38	0.5
1	2	B	1727	medium positional	0.33	0.5
1	3	C	1727	medium positional	0.37	0.5
2	1	A	1600	medium positional	0.31	0.5
2	2	B	1600	medium positional	0.36	0.5
2	3	C	1600	medium positional	0.32	0.5
3	1	D	1727	medium positional	0.35	0.5
3	2	E	1727	medium positional	0.35	0.5
3	3	F	1727	medium positional	0.43	0.5
4	1	D	1600	medium positional	0.31	0.5
4	2	E	1600	medium positional	0.33	0.5
4	3	F	1600	medium positional	0.34	0.5
1	1	A	1727	medium thermal	0.55	2
1	2	B	1727	medium thermal	0.58	2
1	3	C	1727	medium thermal	0.55	2
2	1	A	1600	medium thermal	0.47	2
2	2	B	1600	medium thermal	0.46	2
2	3	C	1600	medium thermal	0.45	2
3	1	D	1727	medium thermal	0.49	2
3	2	E	1727	medium thermal	0.49	2
3	3	F	1727	medium thermal	0.49	2
4	1	D	1600	medium thermal	0.49	2
4	2	E	1600	medium thermal	0.52	2
4	3	F	1600	medium thermal	0.5	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.344	197
R_work	0.24	9652

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	1.2828	0.3253	-0.1381	1.4573	0.3802	1.2355	0.0051	-0.0977	-0.1897	0.0747	0.0274	-0.1316	0.2685	0.1305	-0.0325	-0.2209	0.0247	-0.0339	-0.1276	0.0188	-0.0758	-17.486	-21.87	-46.384
2	1.5223	-0.7605	-0.2364	3.2724	0.1052	1.5583	-0.0052	-0.1164	0.1516	0.0199	-0.0405	0.0398	-0.1618	-0.0109	0.0457	-0.2669	-0.0292	-0.0037	-0.1319	-0.0499	-0.1007	-26.47	6.572	-40.38
3	1.5601	-0.1467	-0.1972	1.0996	-0.0975	2.7033	-0.0333	-0.0308	0.1698	0.1194	0.057	-0.0089	-0.2052	0.0246	-0.0237	-0.2731	-0.0308	-0.0051	-0.1051	0.007	-0.0891	-17.244	66.477	-26.426
4	1.3866	0.6415	0.9832	2.2208	0.788	3.5323	-0.0306	0.1167	-0.0079	-0.1941	0.0575	0.0399	0.0549	-0.1156	-0.027	-0.3114	0.0046	0.013	-0.0518	0.0338	-0.1091	-26.467	56.836	-53.843
5	1.0314	-0.1761	0.296	1.8444	-0.1781	1.2838	0.0286	0.1444	-0.0042	-0.247	-0.0609	-0.1394	-0.0255	0.1065	0.0323	-0.2894	0.0102	0.0373	-0.1236	-0.0022	-0.0911	-17.568	39.561	-112.558
6	1.4268	0.7549	-0.9503	2.0118	-0.9274	2.8996	-0.0142	-0.089	-0.1266	0.0324	-0.0121	-0.0463	0.084	0.0577	0.0263	-0.2632	0.0196	-0.021	-0.1723	0.0229	-0.0525	-26.149	20.187	-90.879
7	1.0528	0.6836	0.2803	2.148	-0.5274	2.695	-0.0634	0.0091	0.053	-0.0198	0.1754	0.1855	-0.4847	-0.6189	-0.112	-0.2413	0.1138	0.0155	0.0098	0.0232	-0.1212	-33.766	73.463	-101.97
8	1.619	-0.5476	0.7222	0.9775	-0.7481	2.8303	-0.0227	-0.1401	-0.016	0.1884	0.0232	0.0854	-0.2195	-0.1939	-0.0005	-0.2189	-0.0084	0.0114	-0.1048	-0.0047	-0.1228	-22.348	60.168	-77.513
9	1.0471	-0.3617	-0.3805	2.2447	0.1326	1.9635	-0.0072	0.069	-0.1671	-0.2734	0.0463	0.2298	0.4062	0.0706	-0.0391	-0.1016	0.0084	-0.095	-0.1388	-0.0178	-0.0532	-33.433	-29.916	-80.948
10	1.7822	1.1765	0.1297	2.3483	-0.0543	0.6143	-0.0354	0.1231	0.1105	-0.1548	0.0354	0.0783	0.0387	0.0171	-0.0001	-0.2039	0.0296	-0.0074	-0.115	0.0288	-0.0822	-22.136	-2.11	-81.811
11	1.1735	-0.4641	0.2968	1.6727	0.7913	3.602	-0.1906	0.0267	0.0042	0.3093	-0.1302	0.2103	0.3063	-0.2187	0.3208	-0.2029	-0.0463	0.0796	-0.1349	-0.0406	-0.071	-33.15	40.857	-2.092
12	2.1405	-1.0258	-1.6801	2.4085	2.3134	2.7656	-0.159	0.1048	-0.16	0.3906	-0.0178	0.2371	0.5088	-0.1367	0.1768	-0.1329	-0.0397	0.0184	-0.1445	-0.0076	-0.0825	-21.949	25.599	-25.488

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 221
2	X-RAY DIFFRACTION	2	A	222 - 432
3	X-RAY DIFFRACTION	3	B	1 - 221
4	X-RAY DIFFRACTION	4	B	222 - 432
5	X-RAY DIFFRACTION	5	C	1 - 221
6	X-RAY DIFFRACTION	6	C	222 - 432
7	X-RAY DIFFRACTION	7	D	1 - 221
8	X-RAY DIFFRACTION	8	D	222 - 432
9	X-RAY DIFFRACTION	9	E	1 - 221
10	X-RAY DIFFRACTION	10	E	222 - 432
11	X-RAY DIFFRACTION	11	F	1 - 221
12	X-RAY DIFFRACTION	12	F	222 - 432

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