PDB-6mgd: Thermosulfurimonas dismutans KpsC, beta Kdo 2,7 transferase

ID or keywords:

Entry

Database: PDB / ID: 6mgd

Title

Thermosulfurimonas dismutans KpsC, beta Kdo 2,7 transferase

Components

Capsular polysaccharide export system protein KpsC

Keywords

TRANSFERASE /

glycosyltransferase / cytosine monophosphate

Function / homology

Capsule polysaccharide biosynthesis / Capsule polysaccharide biosynthesis protein / polysaccharide transport / polysaccharide biosynthetic process / Capsular polysaccharide export system protein KpsC

Function and homology information

Biological species

Thermosulfurimonas dismutans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Doyle, L. / Mallette, E. / Kimber, M.S. / Whitfield, C.

Funding support

Canada, 3items

Organization	Grant number	Country
Natural Sciences and Engineering Research Council (NSERC, Canada)	04045-2015	Canada
Canadian Institutes of Health Research (CIHR)	201509FDN-353054	Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)		Canada

Citation

Journal: Nat.Chem.Biol. / Year: 2019
Title: Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules.
Authors: Doyle, L. / Ovchinnikova, O.G. / Myler, K. / Mallette, E. / Huang, B.S. / Lowary, T.L. / Kimber, M.S. / Whitfield, C.

History

Deposition	Sep 13, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2	May 8, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3	May 15, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4	May 29, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5	Nov 27, 2019	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.6	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6mgd.cif.gz	254.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6mgd.ent.gz	208 KB	Display	PDB format
PDBx/mmJSON format	6mgd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgd ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgd	HTTPS FTP

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Related structure data

Related structure data	6mgbC 6mgcC C: citing same article (ref.)
Similar structure data	5o0v-d 1ru4-d 5ia0-3 2a3a-1 4ld5-3 6iy9-1 4qp2-2 3exq-1 2hke-1 6fjz-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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Capsular polysaccharide export system protein KpsC

B: Capsular polysaccharide export system protein KpsC

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

1

A: Capsular polysaccharide export system protein KpsC

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

2

B: Capsular polysaccharide export system protein KpsC

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

Unit cell

Length a, b, c (Å)	55.670, 79.820, 77.400
Angle α, β, γ (deg.)	90.00, 109.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Capsular polysaccharide export system protein KpsC / KpsC beta(2 / 7)Kdo transferase Mass: 38283.238 Da / Num. of mol.: 2 / Fragment: UNP residues 1-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosulfurimonas dismutans (bacteria) Gene: TDIS_1054 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179D3Y0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Capsular polysaccharide export system protein KpsC / KpsC beta(2 / 7)Kdo transferase

Mass: 38283.238 Da / Num. of mol.: 2 / Fragment: UNP residues 1-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermosulfurimonas dismutans (bacteria)
Gene: TDIS_1054 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179D3Y0

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, 10% v/v PEG6000, 5 mg/mL protein with 1 mM CMP, 50 mM L-Arg

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97857 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: May 24, 2018
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 22210 / % possible obs: 99.8 % / Redundancy: 7.6 % / R_sym value: 0.062 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.5→2.55 Å / Mean I/σ(I) obs: 2.2 / R_sym value: 0.85 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→37.299 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.72

	R_factor	Num. reflection	% reflection
R_free	0.2599	1111	5 %
R_work	0.2288	-	-
obs	0.2304	22210	99.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→37.299 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4785	0	0	90	4875

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4891
X-RAY DIFFRACTION	f_angle_d	0.562	6613
X-RAY DIFFRACTION	f_dihedral_angle_d	19.333	2966
X-RAY DIFFRACTION	f_chiral_restr	0.043	739
X-RAY DIFFRACTION	f_plane_restr	0.004	832

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 (%)
2.5-2.6138	0.3534	137	0.3222	2598	X-RAY DIFFRACTION	99
2.6138-2.7515	0.3272	138	0.299	2619	X-RAY DIFFRACTION	99
2.7515-2.9239	0.3368	138	0.279	2635	X-RAY DIFFRACTION	100
2.9239-3.1495	0.2862	138	0.272	2606	X-RAY DIFFRACTION	100
3.1495-3.4663	0.2755	140	0.2516	2651	X-RAY DIFFRACTION	100
3.4663-3.9673	0.263	138	0.2281	2636	X-RAY DIFFRACTION	100
3.9673-4.9965	0.2312	140	0.1905	2649	X-RAY DIFFRACTION	100
4.9965-37.3028	0.2252	142	0.2004	2705	X-RAY DIFFRACTION	100

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	6.472	0.6785	-0.058	6.5394	2.0641	5.2408	-0.4675	0.6738	-0.3508	-0.0049	0.3727	0.3884	0.6926	-0.3808	0.1361	0.5272	-0.0629	0.0853	0.6601	0.003	0.3642	-30.628	6.6962	34.2594
2	7.291	1.1174	1.7618	6.465	1.1778	5.4759	-0.7762	2.0395	-0.0459	-1.1942	0.5077	0.2983	0.3385	0.02	0.2834	0.7324	-0.2274	0.0167	0.9907	0.0068	0.5192	-32.1607	8.5843	23.5506
3	8.4855	0.8501	2.0642	8.5875	3.9866	5.8171	-0.0143	0.4021	0.269	-0.3115	0.2664	-0.0685	-0.125	0.6029	-0.4176	0.6331	-0.2384	0.0021	0.5903	0.0254	0.4721	-22.7194	15.2902	29.0775
4	5.5149	0.8165	-1.6888	2.9067	1.705	1.6881	-0.2115	-0.0467	-0.3051	-0.4219	0.2457	-0.0488	0.9717	0.59	-0.0595	0.8278	0.0279	0.0652	0.8086	0.0633	0.3422	-21.7506	19.3839	36.0169
5	8.0155	-1.0292	1.2443	4.9374	0.6608	8.688	-0.3114	-0.6104	1.1515	-0.1499	0.0978	-0.0919	-1.9379	-0.8867	0.3393	0.6185	0.0273	0.0027	0.5836	-0.081	0.4449	-25.2512	32.0063	46.4436
6	1.411	-0.9327	-0.8804	2.1597	-0.6454	2.8301	0.4601	-0.9047	-0.2905	0.8192	-0.3488	-0.1383	0.3957	-0.0209	0.2081	0.7847	-0.1183	0.0608	0.9985	0.014	0.4249	-1.4501	21.7468	47.1769
7	6.6308	2.0393	-0.1636	4.2919	1.2658	7.5645	0.2581	-0.3523	-0.5013	0.3283	-0.0665	-0.8577	0.3747	1.0127	-0.0591	0.4842	0.0254	-0.0461	0.7809	0.018	0.3966	2.86	20.6528	40.6768
8	4.3152	-0.8618	1.2737	4.417	1.9487	2.1876	-0.3475	-0.886	-0.6725	1.1547	0.2537	0.1289	0.9967	0.111	0.0396	0.6845	-0.0196	0.0311	0.9752	-0.0233	0.4967	-4.9502	23.7036	49.4203
9	4.905	0.6644	-0.7376	3.6791	-0.1432	2.9183	0.1155	0.1186	0.3244	0.1296	0.0827	0.308	-0.3767	-0.2031	-0.1136	0.4057	-0.0205	-0.012	0.5454	-0.0474	0.2095	-21.1996	25.8236	43.7702
10	4.8955	0.3776	-3.1659	6.5832	-1.8246	6.6838	0.1032	-0.3716	0.2003	0.0889	0.2593	-0.5544	-0.9666	0.6872	-0.4717	0.6479	0.0066	0.1021	0.554	-0.1644	0.3788	17.2107	47.5253	9.3989
11	9.5627	-0.7027	1.0145	7.7716	-1.9773	8.1599	0.2633	1.2548	0.3421	-0.7481	0.1872	-0.5975	-0.7155	0.9772	-0.4792	0.7053	0.0595	0.16	0.7404	-0.0358	0.4374	21.9319	43.513	-2.5866
12	4.7209	1.5437	-0.5712	7.5483	-2.5661	9.2002	-0.2377	-0.7554	0.0233	0.2202	0.5563	0.1939	-0.6941	-0.1694	-0.2323	0.4818	0.0287	0.0241	0.603	-0.0396	0.2858	9.635	37.8836	9.1048
13	4.6021	-1.535	-0.4217	3.1819	-1.1451	5.9639	0.5698	0.4341	-0.7565	-0.3949	-0.3308	0.0558	0.9392	1.1968	-0.179	0.4755	0.1103	-0.0381	0.5706	-0.0928	0.4211	11.9858	25.3479	4.3327
14	5.5004	-2.1571	2.2138	0.9654	-1.6378	3.674	0.1517	-0.7745	-0.7884	0.1237	0.1981	0.4648	-0.0443	-0.9198	-0.3558	0.6412	-0.1299	0.0559	0.6534	-0.0141	0.436	-8.5481	26.1727	12.2462
15	8.367	1.1783	0.268	1.869	-0.3246	3.8424	0.428	0.3272	-0.5736	-0.1019	-0.3067	-0.0034	0.5221	-0.4272	-0.1716	0.5305	-0.0204	-0.0366	0.5936	-0.101	0.3925	-10.782	29.4949	-6.4714
16	6.7444	-0.0638	0.2418	4.9484	-3.0031	7.9702	-0.0656	0.5464	0.3223	-0.0704	0.236	0.1906	-1.6637	-1.0298	-0.0394	0.5818	0.1272	-0.0054	1.0628	-0.143	0.4903	-17.9514	38.0196	-2.1105
17	6.059	6.0451	-4.9826	6.135	-5.3688	4.7221	0.9713	-2.3339	1.269	1.1163	-0.4852	0.8252	-0.7942	0.1663	-0.4861	0.6415	-0.0283	0.0709	1.1154	-0.0425	0.5199	-12.8317	27.6375	6.2495
18	4.8097	-0.3033	-0.8938	1.0715	-1.6365	8.404	-0.0091	0.082	-0.3243	0.3511	-0.0985	-0.0814	0.8073	-0.1092	0.1212	0.5655	-0.0879	0.0278	0.3836	-0.0551	0.4114	-0.4637	21.9294	3.5747
19	2.378	1.6597	1.3444	5.9149	1.3987	6.8626	0.0075	-0.4771	0.1964	0.5404	0.125	0.0724	-0.0417	0.1902	-0.0999	0.5267	-0.0063	0.0403	0.578	0.0142	0.4066	5.6476	35.5873	22.0662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 49 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 77 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 78 through 104 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 105 through 133 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 134 through 169 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 170 through 218 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 219 through 259 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 260 through 323 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 30 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 31 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 92 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 93 through 116 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 117 through 165 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 166 through 197 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 198 through 229 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 230 through 244 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 245 through 293 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 294 through 323 )

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