PDB-7a26: Structure of soluble SmhA crystal form 1 of the tripartite alpha-...

ID or keywords:

Entry

Database: PDB / ID: 7a26

Title

Structure of soluble SmhA crystal form 1 of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.

Components

SmhA

Keywords

TOXIN / Pore forming toxin / Bacterial toxin / Serratia marcescens

Function / homology

metal ion binding / HBL/NHE enterotoxin family protein

Function and homology information

Biological species

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.98 Å

Authors

Churchill-Angus, A.M. / Baker, P.J.

Citation

Journal: Sci Rep / Year: 2021
Title: Characterisation of a tripartite alpha-pore forming toxin from Serratia marcescens
Authors: Churchill-Angus, A.M. / Schofield, T.H.B. / Marlow, T.R. / Sedelnikova, S.E. / Wilson, J.S. / Rafferty, J.B. / Baker, P.J.

History

Deposition	Aug 16, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7a26.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb7a26.ent.gz		Display	PDB format
PDBx/mmJSON format	7a26.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7a26_validation.pdf.gz	504.1 KB	Display	wwPDB validaton report
Full document	7a26_full_validation.pdf.gz	530.5 KB	Display
Data in XML	7a26_validation.xml.gz	99.3 KB	Display
Data in CIF	7a26_validation.cif.gz	126 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a2/7a26 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/7a26	HTTPS FTP

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Related structure data

Related structure data	6zz5C 6zzhC 7a0gC 7a27C C: citing same article (ref.)
Similar structure data	1xl3-2 7a27-1 7a27-3 7a27-2 3ljn-d 3lh8-1 3lha-1 6hem-d 1zb1-2 3ffl-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) 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

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: SmhA

BBB: SmhA

CCC: SmhA

EEE: SmhA

FFF: SmhA

GGG: SmhA

HHH: SmhA

DDD: SmhA

hetero molecules

324 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: SmhA

defined by author
Evidence: gel filtration
40.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: SmhA

hetero molecules

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

3

CCC: SmhA

hetero molecules

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

4

EEE: SmhA

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

5

FFF: SmhA

hetero molecules

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

6

GGG: SmhA

hetero molecules

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

7

HHH: SmhA

hetero molecules

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

8

DDD: SmhA

hetero molecules

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

Unit cell

Length a, b, c (Å)	151.364, 151.364, 133.456
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	77
Space group name H-M	P4₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	SmhA Mass: 40398.328 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: BHU62_20100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4NVM5
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.54 %
Crystal grow	Temperature: 280 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 0.16 M CaCl2 and 20 % PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.98→67.692 Å / Num. obs: 61518 / % possible obs: 100 % / Redundancy: 28.1 % / CC_1/2: 1 / R_merge(I) obs: 0.406 / R_pim(I) all: 0.078 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.98→3.03 Å / R_merge(I) obs: 3.048 / Num. unique obs: 3065 / CC_1/2: 0.6 / R_pim(I) all: 0.575

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
DIALS		data reduction
DIALS		data scaling
CRANK		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.98→67.692 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.917 / WR_factor R_free: 0.232 / WR_factor R_work: 0.198 / SU B: 46.667 / SU ML: 0.367 / Average fsc free: 0.8862 / Average fsc work: 0.9006 / Cross valid method: FREE R-VALUE / ESU R Free: 0.455
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2539	3051	4.962 %
R_work	0.2196	58431	-
all	0.221	-	-
obs	-	61482	99.967 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 62.893 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.356 Å²	-0 Å²	-0 Å²
2-	-	1.356 Å²	-0 Å²
3-	-	-	-2.713 Å²

Refinement step

Cycle: LAST / Resolution: 2.98→67.692 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20420	0	9	34	20463

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	20656
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	19332
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	1.625	28049
X-RAY DIFFRACTION	r_angle_other_deg	1.305	1.56	44973
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.273	5	2723
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.709	26.681	904
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.519	15	3343
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.578	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2903
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	23319
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3550
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	4637
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.169	0.2	16709
X-RAY DIFFRACTION	r_nbtor_refined	0.154	0.2	10441
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	9575
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	220
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	50
X-RAY DIFFRACTION	r_nbd_other	0.253	0.2	147
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.361	0.2	15
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.18	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.392	4.451	10952
X-RAY DIFFRACTION	r_mcbond_other	1.393	4.451	10951
X-RAY DIFFRACTION	r_mcangle_it	2.44	6.675	13655
X-RAY DIFFRACTION	r_mcangle_other	2.44	6.675	13656
X-RAY DIFFRACTION	r_scbond_it	1.355	4.489	9701
X-RAY DIFFRACTION	r_scbond_other	1.355	4.489	9702
X-RAY DIFFRACTION	r_scangle_it	2.263	6.686	14394
X-RAY DIFFRACTION	r_scangle_other	2.263	6.686	14394
X-RAY DIFFRACTION	r_lrange_it	4.212	53.719	22766
X-RAY DIFFRACTION	r_lrange_other	4.212	53.72	22767
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	10665
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.094	0.05	10687
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.091	0.05	10813
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.086	0.05	10785
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.099	0.05	10741
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.087	0.05	10769
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.109	0.05	9307
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.094	0.05	10669
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.095	0.05	10671
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.096	0.05	10614
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.086	0.05	10862
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.095	0.05	10641
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.107	0.05	9335
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.102	0.05	10644
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.099	0.05	10649
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.103	0.05	10709
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.098	0.05	10676
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.106	0.05	9388
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.093	0.05	10736
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.1	0.05	10775
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.092	0.05	10767
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.114	0.05	9275
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.106	0.05	10705
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.084	0.05	10801
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.11	0.05	9333
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.098	0.05	10745
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.099	0.05	9415
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.106	0.05	9325

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.98-3.057	0.331	228	0.335	4273	0.335	4509	0.763	0.775	99.8226	0.329
3.057-3.141	0.346	216	0.316	4161	0.317	4379	0.761	0.792	99.9543	0.308
3.141-3.232	0.311	257	0.303	4054	0.303	4313	0.813	0.822	99.9536	0.291
3.232-3.331	0.306	170	0.282	3982	0.283	4154	0.845	0.866	99.9519	0.268
3.331-3.44	0.281	206	0.264	3819	0.265	4025	0.896	0.89	100	0.25
3.44-3.56	0.288	207	0.256	3727	0.257	3934	0.874	0.893	100	0.235
3.56-3.694	0.28	194	0.241	3567	0.243	3761	0.896	0.904	100	0.221
3.694-3.845	0.265	184	0.222	3433	0.224	3617	0.914	0.917	100	0.203
3.845-4.015	0.229	176	0.192	3307	0.193	3483	0.933	0.95	100	0.173
4.015-4.21	0.219	182	0.185	3186	0.187	3368	0.94	0.951	100	0.168
4.21-4.437	0.188	166	0.172	3015	0.173	3181	0.95	0.956	100	0.156
4.437-4.705	0.242	125	0.166	2861	0.169	2986	0.938	0.959	100	0.152
4.705-5.028	0.218	127	0.186	2705	0.187	2833	0.943	0.953	99.9647	0.17
5.028-5.428	0.217	114	0.201	2526	0.201	2640	0.952	0.959	100	0.184
5.428-5.943	0.315	97	0.248	2333	0.25	2430	0.907	0.932	100	0.231
5.943-6.638	0.277	116	0.216	2101	0.219	2217	0.916	0.94	100	0.201
6.638-7.652	0.205	92	0.168	1841	0.17	1933	0.956	0.963	100	0.158
7.652-9.342	0.174	82	0.153	1583	0.154	1665	0.974	0.975	100	0.149
9.342-13.088	0.186	67	0.16	1232	0.161	1299	0.97	0.982	100	0.16
13.088-67.692	0.378	45	0.312	725	0.315	770	0.887	0.918	100	0.332

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	2.185	-0.2715	-2.4243	0.3689	0.106	3.9876	0.1052	0.0967	0.0421	-0.0054	-0.0514	0.0693	-0.3277	-0.1933	-0.0538	0.0866	-0.0214	0.003	0.062	-0.0311	0.2758	79.9746	50.4479	58.4697
2	1.1186	0.8633	-1.3815	2.1245	-1.9038	3.6732	0.1182	0.0687	0.043	0.0937	-0.0351	0.2049	-0.2594	-0.149	-0.0832	0.0338	0.0335	-0.0397	0.0448	-0.0663	0.1457	102.2006	4.5511	11.3159
3	2.0183	-0.8082	1.6424	1.9099	-1.6887	5.2008	0.082	-0.1131	-0.0026	-0.0454	0.0354	-0.0906	0.253	-0.154	-0.1174	0.062	-0.0421	0.0107	0.0314	-0.0121	0.2908	67.0433	27.5758	39.5575
4	2.4551	0.0656	-2.9858	0.1259	-0.2901	4.0747	0.147	0.1488	0.0924	0.0093	0.0167	0.1069	-0.215	-0.2435	-0.1637	0.1607	-0.0837	-0.0102	0.186	0.0208	0.3368	79.9386	50.4459	-3.8994
5	0.3069	-0.3577	-0.5985	2.8262	3.1202	4.8504	-0.0553	-0.0236	-0.0064	-0.0582	-0.0066	-0.0056	-0.0734	0.3319	0.0619	0.0304	0.0153	0.0037	0.1252	0.0231	0.079	126.4359	-6.6523	31.1157
6	1.3091	0.969	-1.5656	2.1537	-2.1857	3.9127	0.1828	-0.1042	-0.0145	0.3228	-0.0846	0.1785	-0.3687	0.0413	-0.0982	0.0941	-0.0341	-0.0083	0.0852	-0.076	0.1735	101.7846	4.9213	73.7967
7	2.4304	0.5078	3.2364	0.3239	0.7806	4.5378	-0.0233	0.0917	0.0377	-0.1178	-0.0369	0.0111	-0.0153	0.1944	0.0602	0.2319	-0.0671	0.0348	0.193	0.01	0.1439	144.6926	24.7429	35.4833
8	2.8868	1.1367	1.9035	2.0383	1.8866	5.768	-0.0325	-0.3868	0.6344	0.3291	-0.1342	0.0793	0.2062	0.2912	0.1667	0.1793	0.0639	0.062	0.1692	-0.0729	0.4519	123.2079	66.0742	32.8273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 366
2	X-RAY DIFFRACTION	2	ALL	BBB	2 - 401
3	X-RAY DIFFRACTION	3	ALL	CCC	2 - 367
4	X-RAY DIFFRACTION	4	ALL	EEE	2 - 367
5	X-RAY DIFFRACTION	5	ALL	FFF	2 - 367
6	X-RAY DIFFRACTION	6	ALL	GGG	2 - 367
7	X-RAY DIFFRACTION	7	ALL	HHH	2 - 367
8	X-RAY DIFFRACTION	8	ALL	DDD	2 - 366

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