PDB-7a0g: Structure of the SmhB pore of the tripartite alpha-pore forming t...

ID or keywords:

Entry

Database: PDB / ID: 7a0g

Title

Structure of the SmhB pore of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.

Components

SmhB

Keywords

TOXIN / Pore / Pore forming toxin / Bacterial toxin / Serratia marcescens

Function / homology

Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / membrane / HBL/NHE enterotoxin family protein

Function and homology information

Biological species

Serratia marcescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 6.979 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 8, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7a0g.cif.gz	645.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7a0g.ent.gz		Display	PDB format
PDBx/mmJSON format	7a0g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7a0g_validation.pdf.gz	475.5 KB	Display	wwPDB validaton report
Full document	7a0g_full_validation.pdf.gz	480.5 KB	Display
Data in XML	7a0g_validation.xml.gz	73.9 KB	Display
Data in CIF	7a0g_validation.cif.gz	107.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/7a0g ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0g	HTTPS FTP

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Related structure data

Related structure data	6zz5C 6zzhC 7a26C 7a27C 6grjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6h2f-d 6grj-d 2502 6zca-d 4890 2808 11104 21921 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

Deposited unit

AAA: SmhB

BBB: SmhB

CCC: SmhB

DDD: SmhB

EEE: SmhB

FFF: SmhB

GGG: SmhB

HHH: SmhB

III: SmhB

JJJ: SmhB

394 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	224.481, 118.062, 209.532
Angle α, β, γ (deg.)	90.000, 109.438, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	SmhB / SmhB Mass: 39376.562 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Details: Residues for each chain are left as poly-alanine as density for side chains could not be resolved at this resolution. Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: BHU62_20105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4NVM7

#1: Protein

SmhB / SmhB

Mass: 39376.562 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: Residues for each chain are left as poly-alanine as density for side chains could not be resolved at this resolution.
Source: (gene. exp.)

Serratia marcescens (bacteria) / Gene: BHU62_20105 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4NVM7

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 63.81 %
Crystal grow	Temperature: 280.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Calcium chloride, 40% MPD

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 6.979→66.769 Å / Num. all: 28759 / Num. obs: 8304 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC_1/2: 0.7 / R_merge(I) obs: 2.295 / R_pim(I) all: 1.403 / Net I/σ(I): 1.3
Reflection shell	Resolution: 6.979→7.1 Å / R_merge(I) obs: 3.384 / Num. unique obs: 350 / CC_1/2: 0.5 / R_pim(I) all: 2.356

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6GRJ

6grj

Resolution: 6.979→66.769 Å / Cor.coef. F_o:F_c: 0.747 / Cor.coef. F_o:F_c free: 0.726 / WR_factor R_free: 0.386 / WR_factor R_work: 0.388 / SU B: 1350.051 / SU ML: 10.26 / Average fsc free: 0.7133 / Average fsc work: 0.7476 / Cross valid method: FREE R-VALUE / ESU R Free: 3.382
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3351	424	5.106 %
R_work	0.3341	7880	-
all	0.334	-	-
obs	-	8304	98.693 %

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: 0.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	8.38 Å²	-0 Å²	5.016 Å²
2-	-	29.781 Å²	-0 Å²
3-	-	-	-33.385 Å²

Refinement step

Cycle: LAST / Resolution: 6.979→66.769 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15778	0	0	0	15778

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	15762
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.019	9461
X-RAY DIFFRACTION	r_angle_refined_deg	1.496	1.617	21821
X-RAY DIFFRACTION	r_angle_other_deg	1.63	1.617	20283
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.108	5	3211
X-RAY DIFFRACTION	r_chiral_restr	0.025	0.2	2867
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	22320
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3160
X-RAY DIFFRACTION	r_nbd_refined	0.187	0.2	4131
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.154	0.2	4878
X-RAY DIFFRACTION	r_nbtor_refined	0.102	0.2	9148
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	7785
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.066	0.2	228
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.427	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	0	0.05	12894
X-RAY DIFFRACTION	r_mcbond_other	0	0.05	12893
X-RAY DIFFRACTION	r_mcangle_it	0	0.075	16085
X-RAY DIFFRACTION	r_mcangle_other	0	0.075	16086
X-RAY DIFFRACTION	r_scbond_it	0	0.05	2866
X-RAY DIFFRACTION	r_scbond_other	0	0.05	2867
X-RAY DIFFRACTION	r_scangle_it	0	0.075	5733
X-RAY DIFFRACTION	r_scangle_other	0	0.075	5733
X-RAY DIFFRACTION	r_lrange_it	0	0.732	16718
X-RAY DIFFRACTION	r_lrange_other	0	0.732	16719
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	6480
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.016	0.05	6955
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.076	0.05	6458
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.021	0.05	6931
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.077	0.05	6381
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.024	0.05	6950
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.022	0.05	6930
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.08	0.05	6380
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.078	0.05	6483
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.073	0.05	6480
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.018	0.05	6723
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.073	0.05	6468
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.049	0.05	6604
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.074	0.05	6483
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.072	0.05	6453
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.04	0.05	6585
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.031	0.05	6771
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.074	0.05	6453
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.019	0.05	6919
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.076	0.05	6381
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.023	0.05	6938
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.019	0.05	6918
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.078	0.05	6377
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.078	0.05	6479
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.075	0.05	6452
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.047	0.05	6566
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.073	0.05	6459
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.075	0.05	6459
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.042	0.05	6632
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.009	0.05	6722
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.076	0.05	6390
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.017	0.05	6942
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.013	0.05	6934
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.079	0.05	6386
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.075	0.05	6477
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.074	0.05	6385
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.072	0.05	6372
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.045	0.05	6556
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.05	0.05	6608
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.015	0.05	6929
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.078	0.05	6383
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.075	0.05	6481
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.078	0.05	6380
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.074	0.05	6450
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.041	0.05	6581

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
6.979-7.158	0.468	38	0.431	494	0.434	586	0.539	0.667	90.785	0.421
7.158-7.352	0.366	25	0.385	563	0.385	600	0.687	0.671	98	0.39
7.352-7.563	0.29	33	0.349	535	0.346	575	0.732	0.696	98.7826	0.364
7.563-7.792	0.33	34	0.346	517	0.345	561	0.695	0.651	98.2175	0.37
7.792-8.044	0.357	27	0.334	525	0.335	557	0.659	0.643	99.1023	0.355
8.044-8.322	0.362	36	0.336	488	0.338	525	0.52	0.601	99.8095	0.353
8.322-8.631	0.309	22	0.32	482	0.319	506	0.663	0.675	99.6047	0.35
8.631-8.977	0.329	33	0.301	465	0.303	499	0.724	0.783	99.7996	0.322
8.977-9.369	0.231	21	0.287	429	0.284	453	0.879	0.844	99.3378	0.322
9.369-9.816	0.265	22	0.275	452	0.275	474	0.874	0.861	100	0.312
9.816-10.335	0.232	25	0.267	397	0.265	422	0.861	0.874	100	0.306
10.335-10.946	0.274	18	0.268	390	0.268	409	0.852	0.871	99.7555	0.3
10.946-11.679	0.27	16	0.266	388	0.266	404	0.841	0.87	100	0.311
11.679-12.583	0.324	7	0.298	352	0.298	359	0.769	0.845	100	0.343
12.583-13.735	0.278	12	0.293	319	0.293	331	0.792	0.845	100	0.333
13.735-15.275	0.34	17	0.321	287	0.322	304	0.814	0.823	100	0.351
15.275-17.487	0.278	11	0.405	266	0.402	277	0.689	0.749	100	0.419
17.487-21.059	0.559	8	0.433	237	0.437	245	0.545	0.738	100	0.448
21.059-28.402	0.62	10	0.398	173	0.409	183	0.668	0.74	100	0.448
28.402-66.769	0.548	9	0.801	121	0.783	134	0.74	0.619	97.0149	1.807

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