PDB-7a27: Structure of soluble SmhA crystal form 2 of the tripartite alpha-...

ID or keywords:

Entry

Database: PDB / ID: 7a27

Title

Structure of soluble SmhA crystal form 2 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 /

MOLECULAR REPLACEMENT / Resolution: 2.57 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	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

-
Download

PDBx/mmCIF format	7a27.cif.gz	919.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7a27.ent.gz		Display	PDB format
PDBx/mmJSON format	7a27.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7a27_validation.pdf.gz	455.6 KB	Display	wwPDB validaton report
Full document	7a27_full_validation.pdf.gz	463.3 KB	Display
Data in XML	7a27_validation.xml.gz	44.6 KB	Display
Data in CIF	7a27_validation.cif.gz	61.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a2/7a27 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/7a27	HTTPS FTP

-
Related structure data

Related structure data	6zz5C 6zzhC 7a0gC 7a26SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7a26-8 7a26-6 7a26-5 7a26-2 6akg-2 7a26-1 1zb1-2 6akg-1 5mk2-1 3zix-2 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

6zz5C

6zzhC

7a0gC

7a26SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

GGG: SmhA

AAA: SmhA

BBB: SmhA

CCC: SmhA

160 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

GGG: SmhA

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

2

AAA: SmhA

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

3

BBB: SmhA

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

4

CCC: SmhA

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

Unit cell

Length a, b, c (Å)	81.240, 92.580, 221.100
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains GGG AAA
2	2	Chains GGG BBB
3	3	Chains GGG CCC
4	4	Chains AAA BBB
5	5	Chains AAA CCC
6	6	Chains BBB CCC

NCS ensembles :

ID
6
1
2
3
4
5

#1: Protein	SmhA Mass: 39976.277 Da / Num. of mol.: 4 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.69 %
Crystal grow	Temperature: 280 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium nitrate, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9159 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9159 Å / Relative weight: 1
Reflection	Resolution: 2.57→110.55 Å / Num. obs: 53914 / % possible obs: 99.9 % / Redundancy: 13 % / CC_1/2: 1 / R_merge(I) obs: 0.19 / R_sym value: 0.055 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.57→2.61 Å / R_merge(I) obs: 2.129 / Num. unique obs: 2644 / CC_1/2: 0.8 / R_pim(I) all: 0.595

-
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: 7A26

7a26

Resolution: 2.57→110.55 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.958 / SU B: 44.031 / SU ML: 0.363 / Cross valid method: FREE R-VALUE / ESU R: 0.648 / ESU R Free: 0.292
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.247	2611	4.849 %
R_work	0.2357	51236	-
all	0.236	-	-
obs	-	53847	99.75 %

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: 72.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.09 Å²	-0 Å²	0 Å²
2-	-	10.982 Å²	-0 Å²
3-	-	-	-9.892 Å²

Refinement step

Cycle: LAST / Resolution: 2.57→110.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10372	0	0	74	10446

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	10494
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9867
X-RAY DIFFRACTION	r_angle_refined_deg	1.555	1.62	14247
X-RAY DIFFRACTION	r_angle_other_deg	1.295	1.561	22975
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.253	5	1379
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.996	26.71	462
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.581	15	1816
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.544	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1469
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11823
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1793
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	2287
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	7937
X-RAY DIFFRACTION	r_nbtor_refined	0.149	0.2	5220
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4435
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	104
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.212	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.094	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.345	4.929	5540
X-RAY DIFFRACTION	r_mcbond_other	1.345	4.929	5539
X-RAY DIFFRACTION	r_mcangle_it	2.287	7.389	6911
X-RAY DIFFRACTION	r_mcangle_other	2.287	7.389	6912
X-RAY DIFFRACTION	r_scbond_it	1.214	5	4954
X-RAY DIFFRACTION	r_scbond_other	1.213	5	4955
X-RAY DIFFRACTION	r_scangle_it	2.1	7.457	7336
X-RAY DIFFRACTION	r_scangle_other	2.1	7.457	7337
X-RAY DIFFRACTION	r_lrange_it	3.584	58.983	11480
X-RAY DIFFRACTION	r_lrange_other	3.567	58.978	11476
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	10417
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.085	0.05	10503
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.091	0.05	10564
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	10377
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.087	0.05	10463
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.089	0.05	10480

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
2.57-2.637	0.429	192	0.419	3742	0.42	3956	0.476	0.502	99.4439	0.412
2.637-2.709	0.386	192	0.399	3593	0.398	3814	0.465	0.494	99.2396	0.388
2.709-2.787	0.374	189	0.387	3521	0.386	3721	0.501	0.501	99.7044	0.374
2.787-2.873	0.367	187	0.373	3430	0.373	3636	0.449	0.418	99.4774	0.356
2.873-2.967	0.351	144	0.351	3342	0.351	3504	0.586	0.599	99.4863	0.332
2.967-3.071	0.28	142	0.321	3271	0.319	3419	0.734	0.679	99.8245	0.304
3.071-3.187	0.28	151	0.288	3138	0.287	3295	0.826	0.829	99.8179	0.269
3.187-3.317	0.26	175	0.262	2998	0.262	3180	0.874	0.877	99.7799	0.248
3.317-3.465	0.284	167	0.245	2867	0.248	3040	0.891	0.893	99.8026	0.232
3.465-3.634	0.267	142	0.239	2774	0.241	2918	0.909	0.916	99.9315	0.229
3.634-3.83	0.25	125	0.214	2664	0.216	2791	0.923	0.926	99.9283	0.208
3.83-4.062	0.214	121	0.187	2542	0.188	2664	0.938	0.948	99.9625	0.182
4.062-4.342	0.163	107	0.169	2359	0.169	2466	0.966	0.963	100	0.169
4.342-4.689	0.212	113	0.171	2213	0.173	2327	0.949	0.964	99.957	0.177
4.689-5.136	0.253	110	0.199	2054	0.202	2164	0.951	0.96	100	0.209
5.136-5.741	0.249	79	0.234	1873	0.235	1952	0.943	0.949	100	0.245
5.741-6.626	0.304	95	0.217	1650	0.222	1745	0.92	0.941	100	0.236
6.626-8.107	0.173	80	0.153	1420	0.154	1501	0.965	0.973	99.9334	0.178
8.107-11.435	0.126	59	0.149	1123	0.148	1183	0.988	0.981	99.9155	0.175
11.435-110.55	0.22	41	0.273	662	0.27	706	0.965	0.942	99.5751	0.355

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	1.3796	1.3581	-0.3213	3.096	-0.2365	1.3425	0.011	-0.1818	-0.0346	0.0603	-0.207	-0.0139	-0.1022	0.231	0.196	0.201	-0.0213	-0.029	0.2633	0.0239	0.127	-30.8334	-8.0303	15.5311
2	1.0139	0.3736	-0.2393	4.7955	-1.3732	1.3409	-0.1629	0.0437	-0.0134	-0.2399	0.0346	0.0966	0.0764	-0.0275	0.1283	0.2782	0.0194	-0.0244	0.2338	0.0048	0.1224	-29.2876	-5.9713	-13.1925
3	3.8639	0.371	1.0128	0.9582	0.1062	2.2365	0.1186	-0.1695	0.0065	0.0918	-0.1576	0.0357	-0.0031	-0.1937	0.039	0.2633	0.0102	-0.0302	0.0424	-0.0209	0.1846	-25.5694	-17.6767	-41.409
4	3.148	-1.4165	0.5956	1.325	-0.5539	1.7956	-0.0353	-0.1785	-0.0594	0.1008	-0.0137	0.0283	-0.1782	0.0117	0.049	0.3485	0.0122	-0.0727	0.0276	-0.0269	0.2113	-51.4232	29.7119	-40.5282

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	GGG	3 - 367
2	X-RAY DIFFRACTION	2	ALL	AAA	3 - 366
3	X-RAY DIFFRACTION	3	ALL	BBB	2 - 367
4	X-RAY DIFFRACTION	4	ALL	CCC	3 - 366

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi