PDB-6w1w: Crystal Structure of Motility Associated Killing Factor B from Vi...

ID or keywords:

Entry

Database: PDB / ID: 6w1w

Title

Crystal Structure of Motility Associated Killing Factor B from Vibrio cholerae

Components

motility-associated killing factor MakB

Keywords

TOXIN / Tripartite pore forming toxin / Cytotoxin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Non-hemolytic enterotoxin lytic component L1

Function and homology information

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.58 Å

Authors

Kim, Y. / Welk, L. / Jedrzejczak, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: J.Bacteriol. / Year: 2022
Title: A Genomic Island of Vibrio cholerae Encodes a Three-Component Cytotoxin with Monomer and Protomer Forms Structurally Similar to Alpha-Pore-Forming Toxins.
Authors: Herrera, A. / Kim, Y. / Chen, J. / Jedrzejczak, R. / Shukla, S. / Maltseva, N. / Joachimiak, G. / Welk, L. / Wiersum, G. / Jaroszewski, L. / Godzik, A. / Joachimiak, A. / Satchell, K.J.F.

History

Deposition	Mar 4, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2022	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 6, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6w1w.cif.gz	343.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6w1w.ent.gz	238.9 KB	Display	PDB format
PDBx/mmJSON format	6w1w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6w1w_validation.pdf.gz	451.9 KB	Display	wwPDB validaton report
Full document	6w1w_full_validation.pdf.gz	460.8 KB	Display
Data in XML	6w1w_validation.xml.gz	24.6 KB	Display
Data in CIF	6w1w_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1w ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1w	HTTPS FTP

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Related structure data

Related structure data	6dfpC 6w08C C: citing same article (ref.)
Similar structure data	6t8d-d 7a27-3 7a26-6 7a26-8 3lh8-2 3lha-2 7a26-5 2fau-d 7a27-2 1v1o-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP95802

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: motility-associated killing factor MakB

B: motility-associated killing factor MakB

hetero molecules

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

1

A: motility-associated killing factor MakB

hetero molecules

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

2

B: motility-associated killing factor MakB

hetero molecules

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

Unit cell

Length a, b, c (Å)	137.718, 137.718, 233.834
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

#1: Protein	motility-associated killing factor MakB Mass: 39033.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0882 / Plasmid: pMCSG73 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9KL65
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 8 / 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: 8.2 Å³/Da / Density % sol: 85 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium acetate, 0.1 M HEPES-NaOH, pH 7.5, 25% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 27, 2018
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.58→66.05 Å / Num. obs: 81344 / % possible obs: 100 % / Redundancy: 9.7 % / B_iso Wilson estimate: 63.86 Å² / CC_1/2: 0.992 / R_merge(I) obs: 0.139 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.58→2.62 Å / Redundancy: 10.1 % / R_merge(I) obs: 0.953 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 40719 / CC_1/2: 0.78 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.58→66.05 Å / SU ML: 0.6584 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 41.7064

	R_factor	Num. reflection	% reflection
R_free	0.2858	4035	4.98 %
R_work	0.2764	-	-
obs	0.2769	80943	99.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 120.87 Å²

Refinement step

Cycle: LAST / Resolution: 2.58→66.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5367	0	12	8	5387

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	5479
X-RAY DIFFRACTION	f_angle_d	0.5217	7448
X-RAY DIFFRACTION	f_chiral_restr	0.0375	909
X-RAY DIFFRACTION	f_plane_restr	0.0026	948
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0879	3344

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.58-2.61	0.4145	137	0.437	2645	X-RAY DIFFRACTION	99.75
2.61-2.64	0.4101	152	0.436	2603	X-RAY DIFFRACTION	99.96
2.64-2.68	0.4056	140	0.4368	2612	X-RAY DIFFRACTION	99.93
2.68-2.71	0.3994	148	0.4334	2634	X-RAY DIFFRACTION	99.93
2.71-2.75	0.4789	116	0.4344	2644	X-RAY DIFFRACTION	99.93
2.75-2.79	0.4232	118	0.4333	2641	X-RAY DIFFRACTION	100
2.79-2.83	0.4746	148	0.4273	2649	X-RAY DIFFRACTION	99.96
2.83-2.87	0.4035	135	0.4274	2642	X-RAY DIFFRACTION	99.71
2.87-2.92	0.3858	137	0.4361	2630	X-RAY DIFFRACTION	99.46
2.92-2.97	0.481	133	0.4416	2587	X-RAY DIFFRACTION	99.38
2.97-3.02	0.4859	112	0.4817	2663	X-RAY DIFFRACTION	99.61
3.02-3.08	0.536	145	0.5208	2641	X-RAY DIFFRACTION	99.22
3.08-3.15	0.4565	129	0.4586	2639	X-RAY DIFFRACTION	99.32
3.15-3.21	0.4261	147	0.4138	2558	X-RAY DIFFRACTION	98.51
3.21-3.29	0.3985	171	0.3698	2596	X-RAY DIFFRACTION	98.43
3.29-3.37	0.3597	123	0.3514	2644	X-RAY DIFFRACTION	99.14
3.37-3.46	0.386	164	0.3443	2611	X-RAY DIFFRACTION	99.53
3.46-3.56	0.3326	167	0.3256	2604	X-RAY DIFFRACTION	99.28
3.56-3.68	0.3288	151	0.3144	2626	X-RAY DIFFRACTION	99.04
3.68-3.81	0.3283	170	0.3353	2599	X-RAY DIFFRACTION	99
3.81-3.96	0.3208	128	0.2738	2670	X-RAY DIFFRACTION	99.61
3.96-4.14	0.3076	132	0.2454	2647	X-RAY DIFFRACTION	99.5
4.14-4.36	0.2266	127	0.2137	2678	X-RAY DIFFRACTION	99.68
4.36-4.64	0.2398	121	0.1949	2709	X-RAY DIFFRACTION	99.82
4.64-4.99	0.1781	132	0.1854	2706	X-RAY DIFFRACTION	99.86
4.99-5.5	0.2844	123	0.2081	2717	X-RAY DIFFRACTION	100
5.5-6.29	0.2993	152	0.2574	2716	X-RAY DIFFRACTION	100
6.29-7.92	0.1925	110	0.2189	2773	X-RAY DIFFRACTION	99.83
7.92-66.05	0.1532	167	0.1686	2824	X-RAY DIFFRACTION	98.65

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	7.42226466722	5.80763404412	2.55204165542	3.80761417046	0.992700538991	2.22544494539	-0.360349844442	-0.06455613904	0.118746513781	-0.0729821104002	0.310680902245	0.242645259072	-0.422369296277	-0.702978695514	0.297020643175	1.32452339749	-0.0623528826164	0.0939908815222	0.851348461762	0.0398682312261	0.793982795402	51.8370932563	-43.7645129682	-34.557564266
2	4.3486495476	-0.737133446856	-1.24526271471	6.64971713394	-2.52846018681	3.25006115232	0.521888439216	0.30045774387	-0.469223750717	1.41692316705	0.157198026737	-0.555903531099	-1.34034335855	0.165856320133	-0.440990752128	1.37897550061	-0.0565300225747	-0.177220318352	1.26985141428	-0.000882282910992	0.637798179614	73.9275871927	-26.6440217432	-27.2808595273
3	2.71416109572	0.287662407306	1.48821727586	2.55074999616	0.829014005655	5.22722934136	-0.947337375838	1.90257106629	-1.14720895866	1.00123636839	1.4396158076	-1.14329551193	0.322381744162	-0.201365781043	-0.693043463279	0.978038843815	0.0274264929929	0.141560771359	1.25881121056	0.0152543764877	0.991548235081	48.0357727538	-59.0880276852	-27.0739657094
4	1.58012338416	1.012247712	-0.856840925446	1.90848412571	-0.595128525718	2.62274278618	-0.0560227335903	-0.0821534766035	-0.0539467652737	0.00418850933845	0.0709325037261	-0.0504853866196	-0.595553855955	-0.302568750495	-0.0348985836146	1.05184804159	0.0208771565075	-0.0593411371093	1.16224696173	0.0817443422767	0.469245801773	58.6179545871	-34.6231060675	-33.1835763874
5	0.363708815426	0.94244860774	-0.269001875861	4.81016324998	0.42272196823	4.3421138017	-0.331986740414	0.307956140372	0.0681448757461	-0.89777766962	0.0520133207936	-0.0522776669172	-1.19491510063	-0.197853746385	0.112607229979	1.33136942138	-0.0654334770365	-0.110160767553	1.14255352608	0.0923879984286	0.55908428954	69.2177482779	-25.6551591083	-45.7958333747
6	3.76823117643	3.10767050475	-0.863276093361	1.75203951401	-2.51118382132	3.31901695537	-0.283161716454	0.362228551153	0.0318571089309	-0.0107721461507	0.461057350947	0.314294126543	0.35987391177	-1.00761923585	-0.101061575201	1.0793671723	-0.15353043561	0.141555223798	1.31574593226	0.0111304736258	0.67712232806	39.1496419204	-53.7679460824	-28.0142979472
7	5.02696090938	3.31023957986	-1.6272322691	9.97479219554	-2.48228869197	5.33841752591	-0.17112476568	0.0919934495668	-0.584384331411	-0.00799625161704	0.0559346951188	-1.27640754104	-0.265540654746	0.297460403836	0.279558150265	0.983549030641	-0.173802770057	0.0846975118709	1.10498688582	0.0373305605697	0.569041708982	73.1237507031	-37.5965850053	-47.6726915687
8	9.2490870984	-7.66015489083	2.10607612196	5.28411977058	-1.49507399108	1.15775696658	-0.187938884622	0.116468906961	0.160695982852	0.107028318359	0.187221105846	-0.215063059165	-0.550683314662	0.585084156323	0.206930415633	1.31128114255	0.0559299501984	0.0913828346442	0.992483198628	-0.0678526233725	0.746345118516	86.2895136185	-43.9698310157	-4.5243945352
9	3.28445203051	1.34942699912	2.03825108925	4.12946643059	-0.507044051523	2.90605574126	0.582268171756	-0.25856234197	-0.376835204435	-1.84561804085	-0.174027260386	0.502578693452	-1.68297135175	-0.363415174552	-0.196313442599	1.35274774902	0.113743566426	-0.116519857467	1.26080665381	-0.00220799293135	0.598941557838	63.153603188	-25.3037270843	-11.3195857633
10	4.89697744634	-2.40969056151	-1.23539801697	3.19490434696	2.13821715175	3.96486984507	-0.960035043831	-1.17117434069	-1.50836633721	-0.827749350323	1.04747493889	0.785054724999	0.497580090279	0.30919765086	0.372338260013	1.07062892059	-0.0341346615387	0.154617070224	1.22541658157	-0.044297511134	0.997266435403	88.7492221325	-58.2825762495	-12.1400244334
11	4.01990084358	-3.76840556653	-1.88962058164	3.2852706188	1.84960807314	3.22907480882	0.216549835098	0.375156401837	-0.095572546017	-0.357285354711	-0.298417270919	0.103685211042	-0.56126405369	0.411474443098	-0.000793499040222	1.00158691972	-0.117099718546	-0.0792866618073	1.20185846402	-0.115813008438	0.602289025749	83.9477246331	-38.36923661	-15.7547075925
12	0.0854723815032	-0.264073682925	-0.561458893252	3.92690737111	1.16958180601	4.79497769957	-0.234455267866	-0.206518579831	0.103026789276	-0.0278643712894	0.385309414907	-0.265316147002	-0.584235073192	0.175736143916	0.0499935880603	1.15427327046	0.0697926915966	0.0214431587855	1.1687867242	-0.070433605756	0.538470222302	73.010165755	-30.1203240475	6.40395704133
13	0.466855871654	-0.67225465972	-0.0450345929824	4.14608737806	-0.346529137766	3.71425119112	-0.419691242966	-0.443053955055	0.0224446843048	0.952524732634	0.272359686215	0.12640808196	-1.11612888579	0.337966999924	0.152640340528	1.32811387724	0.0734510643708	-0.0781787465446	1.09793393742	-0.0882912310397	0.523138230964	68.716914381	-25.6890826901	6.85198321836
14	4.21980258612	-3.73874408797	-0.553594906679	2.6945540291	1.73883548534	3.57756833317	-0.208483822322	-0.375873965295	0.091450156191	-0.00456300203898	0.362924312124	-0.434664742775	0.34277435425	0.96362085167	-0.0996261712615	0.932076009432	0.110931495318	0.108018064119	1.29906617074	-0.0483537890068	0.63133442594	98.5779415443	-53.7600936938	-10.9396444134
15	5.57744666389	-2.94587573873	-1.73083022111	7.92694623149	1.82239526588	5.33505482776	-0.2108829936	-0.247848127169	-0.356251413028	0.322924596989	0.212327744734	0.938844903348	0.108093556421	-0.417902522971	0.35034711022	0.971596144472	0.179840128738	0.0707049550074	1.07745590983	-0.00593372395445	0.546483590003	64.5485559785	-37.5670481062	8.67181487092

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 65 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 96 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 97 through 207 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 208 through 268 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 269 through 333 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 334 through 354 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 32 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 33 through 63 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 96 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 97 through 153 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 154 through 208 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 209 through 268 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 269 through 333 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 334 through 354 )

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