PDB-7t31: X-ray Structure of Clostridiodies difficile PilW

ID or keywords:

Entry

Database: PDB / ID: 7t31

Title

X-ray Structure of Clostridiodies difficile PilW

Components

Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

Keywords

DNA BINDING PROTEIN / type IV pilin / gram-positive

Function / homology

Function and homology information

protein secretion by the type II secretion system / type II protein secretion system complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...
Similarity search - Function

Biological species

Clostridioides difficile R20291 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Ronish, L.A. / Piepenbrink, K.H.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	K22 AI123467	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P20-GM113126	United States

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Recognition of extracellular DNA by type IV pili promotes biofilm formation by Clostridioides difficile.
Authors: Ronish, L.A. / Sidner, B. / Yu, Y. / Piepenbrink, K.H.

History

Deposition	Dec 6, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7t31.cif.gz	781.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7t31.ent.gz	651.4 KB	Display	PDB format
PDBx/mmJSON format	7t31.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7t31_validation.pdf.gz	467.7 KB	Display	wwPDB validaton report
Full document	7t31_full_validation.pdf.gz	485.7 KB	Display
Data in XML	7t31_validation.xml.gz	75.2 KB	Display
Data in CIF	7t31_validation.cif.gz	107.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t3/7t31 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/7t31	HTTPS FTP

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Related structure data

Related structure data	8dx4C 4ogm 4pe2 4tsm 6t8s C: citing same article (ref.)
Similar structure data	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
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (6) #221 - May 2018 Human Papillomavirus and Vaccines similarity (6) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (6) #211 - Jul 2017 Pilus Machine similarity (3)

Deposited unit

A: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

B: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

C: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

D: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

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

1

A: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

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

2

B: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

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

3

C: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

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

4

D: Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera

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

Unit cell

Length a, b, c (Å)	65.244, 81.754, 102.797
Angle α, β, γ (deg.)	92.31, 91.05, 113.37
Int Tables number	1
Space group name H-M	P1

#1: Protein	Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP Mass: 55989.332 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile R20291 (bacteria) Strain: K12, 630 / Gene: malE, b4034, JW3994, CD630_23050 / Plasmid: petMal / Production host: Escherichia coli (E. coli) / Strain (production host): NiCO21 / References: UniProt: P0AEX9, UniProt: Q185H8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Maltose/maltodextrin-binding periplasmic protein,Putative pilin protein chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP

Mass: 55989.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridioides difficile R20291 (bacteria)
Strain: K12, 630 / Gene: malE, b4034, JW3994, CD630_23050 / Plasmid: petMal / Production host:

Escherichia coli (E. coli) / Strain (production host): NiCO21 / References: UniProt: P0AEX9, UniProt: Q185H8

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 995 / 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: 2.35 Å³/Da / Density % sol: 47.57 % / Description: Rods
Crystal grow	Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes pH 7.5, 25% Peg 3350, 0.0375M NaCl, 0.2M CsCl2, 2% ethanol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2020

Radiation

Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 2.01→74.95 Å / Num. obs: 121248 / % possible obs: 93.1 % / Redundancy: 1.8 % / B_iso Wilson estimate: 28.39 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.074 / R_pim(I) all: 0.074 / R_rim(I) all: 0.104 / Net I/σ(I): 3.1 / Num. measured all: 216621

Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.01-2.12	1.106	33001	18085	0.395	1.105	1.563	0.5	95.1
6.35-74.95	0.031	6825	3868	0.995	0.031	0.044	8.7	94

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3 Å	102.64 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
XDS		data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.0	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MBP, PilA1

Resolution: 2.3→39.7 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2453	3522	4.98 %
R_work	0.1961	-	-
obs	0.1985	70741	81.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→39.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14998	0	0	995	15993

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	15413
X-RAY DIFFRACTION	f_angle_d	0.539	20928
X-RAY DIFFRACTION	f_dihedral_angle_d	18.214	5642
X-RAY DIFFRACTION	f_chiral_restr	0.042	2315
X-RAY DIFFRACTION	f_plane_restr	0.003	2702

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 (%)
2.3-2.33	0.3377	79	0.2594	1429	X-RAY DIFFRACTION	42
2.33-2.36	0.3218	70	0.2483	1576	X-RAY DIFFRACTION	49
2.36-2.4	0.3047	69	0.2508	1839	X-RAY DIFFRACTION	55
2.4-2.44	0.2851	82	0.2324	2018	X-RAY DIFFRACTION	62
2.44-2.48	0.2888	122	0.2437	2168	X-RAY DIFFRACTION	66
2.48-2.52	0.2692	129	0.2441	2362	X-RAY DIFFRACTION	72
2.52-2.57	0.2933	165	0.2564	2521	X-RAY DIFFRACTION	77
2.57-2.62	0.307	148	0.2596	2768	X-RAY DIFFRACTION	84
2.62-2.67	0.2646	138	0.2403	2868	X-RAY DIFFRACTION	88
2.67-2.73	0.3091	167	0.2335	3103	X-RAY DIFFRACTION	93
2.73-2.79	0.308	158	0.2324	3064	X-RAY DIFFRACTION	94
2.79-2.86	0.2962	175	0.2266	3082	X-RAY DIFFRACTION	94
2.86-2.94	0.2896	137	0.2307	3058	X-RAY DIFFRACTION	92
2.94-3.02	0.285	135	0.2275	3015	X-RAY DIFFRACTION	92
3.02-3.12	0.2777	169	0.2304	3011	X-RAY DIFFRACTION	92
3.12-3.23	0.2603	169	0.2185	2945	X-RAY DIFFRACTION	90
3.23-3.36	0.264	170	0.2004	2954	X-RAY DIFFRACTION	91
3.36-3.51	0.2468	141	0.1814	2897	X-RAY DIFFRACTION	87
3.52-3.7	0.2249	136	0.1718	2863	X-RAY DIFFRACTION	87
3.7-3.93	0.2104	158	0.1724	2852	X-RAY DIFFRACTION	87
3.93-4.23	0.1903	179	0.1571	2804	X-RAY DIFFRACTION	86
4.24-4.66	0.1976	150	0.146	2961	X-RAY DIFFRACTION	90
4.66-5.33	0.1931	153	0.1562	2964	X-RAY DIFFRACTION	90
5.33-6.71	0.2391	159	0.1868	3010	X-RAY DIFFRACTION	92
6.72-39.7	0.2129	164	0.1702	3087	X-RAY DIFFRACTION	94

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	6.8796	3.1849	1.1665	6.8079	2.708	5.514	-0.7521	1.5079	0.4577	-1.922	0.4206	0.2984	-0.7462	0.1006	0.2378	0.8144	-0.1758	-0.0857	0.9339	0.0852	0.442	21.0143	-70.5809	23.2892
2	5.6285	1.0095	0.6246	0.6895	-0.0536	1.816	-0.108	-0.0858	0.5841	0.1871	0.133	-0.0156	-0.0171	-0.3523	-0.013	0.3264	0.0609	-0.0453	0.2632	-0.0523	0.3417	33.3775	-72.8603	38.3738
3	7.0013	-1.4152	-1.1548	4.0441	1.0084	2.909	0.2057	0.2395	0.1886	0	-0.0796	0.1581	-0.2088	0.0034	-0.1296	0.2175	0.0599	-0.0017	0.2192	-0.0668	0.3861	54.8014	-71.2591	38.8088
4	2.8036	-0.3975	-0.47	0.2243	-0.3581	1.0198	0.1306	0.0773	-0.2592	0.0107	0.1162	-0.0854	-0.1992	-0.0633	-0.209	0.2766	0.1026	0.0522	0.3068	-0.0901	0.4756	36.1211	-68.4129	44.5347
5	7.0805	1.2455	-2.0164	4.8901	-0.8153	7.8867	0.9854	-1.9415	0.5908	0.6723	-0.1819	-0.1963	-1.5464	0.3328	-0.6222	0.9051	0.0649	0.0589	1.1573	-0.201	0.61	28.392	-46.7706	82.6554
6	4.537	-4.0524	-1.4363	5.3734	2.8535	5.8007	0.3122	-1.5612	1.4355	0.4752	0.469	0.1328	-0.9599	0.5153	-0.6383	1.0401	0.2079	0.3741	0.7685	-0.1748	1.0654	31.7262	-41.1001	73.4472
7	5.8784	-3.8321	-1.2897	5.2163	0.2137	8.5196	0.2376	-0.0933	2.8091	-0.163	-0.137	-0.8823	-1.5363	0.4834	-0.2449	1.2232	0.0564	0.3986	0.5296	-0.0419	1.4923	33.2842	-38.1355	63.7932
8	6.4309	-0.0101	0.8347	0.7283	0.4275	1.2811	0.0314	-1.0035	-0.8938	0.1918	0.0911	-0.2838	0.1133	0.1015	-0.0782	0.2232	0.0292	-0.0524	0.3269	0.0853	0.3563	47.086	-38.1372	36.2362
9	4.4408	0.1138	0.4065	0.6959	0.2466	0.7309	0.04	-0.0546	-0.2493	0.0646	-0.0591	0.0366	0.0695	-0.0288	0.0111	0.1684	-0.0109	-0.0118	0.1428	0.0072	0.0907	25.3259	-32.5058	33.427
10	0.3428	0.1475	0.4204	1.1086	0.5448	1.1929	0.1224	-0.2217	-0.0588	0.4287	-0.1283	-0.2808	0.0717	-0.2004	-0.0319	0.3314	-0.0443	-0.106	0.4994	-0.0322	0.2299	32.975	-22.4505	54.0914
11	6.5321	3.5685	-0.0181	3.3878	0.1933	7.0447	0.1691	0.3818	2.6631	-0.0326	0.4394	-0.155	-1.5295	-0.3916	-0.0414	0.9099	-0.0616	-0.0644	0.7033	-0.0745	1.3939	45.2091	-0.6225	71.2113
12	6.8832	1.4577	1.7506	4.2311	-0.2664	5.2302	0.4551	-1.4766	0.4481	0.9689	-0.3601	0.1662	-0.0233	-0.5971	-0.0554	1.0297	-0.3547	-0.4157	1.2873	0.204	0.5032	39.707	-13.9491	78.3535
13	5.3446	0.0995	-0.4445	0.4963	0.3554	0.9303	0.0098	-0.2782	-0.6511	0.0987	-0.0829	0.0036	0.1704	-0.1976	0.0405	0.2856	-0.0664	0.0446	0.2146	0.0311	0.265	28.5334	-63.2652	105.2464
14	5.6147	0.7917	1.3274	4.0002	1.0581	3.8681	0.2048	0.5699	0.016	-0.252	0.0153	0.2007	0.252	-0.0531	-0.1907	0.2342	0.0298	0.014	0.1808	-0.0088	0.1376	53.0863	-65.4922	93.0604
15	4.2434	0.1712	-0.2	0.1387	0.1555	0.5347	0.1781	-0.4662	0.4584	0.0308	-0.1015	0.0321	-0.0179	-0.0765	-0.0577	0.2039	-0.0535	0.0441	0.1761	-0.053	0.2846	40.6694	-58.4759	106.6958
16	2.2213	0.93	0.6876	0.3559	0.1465	0.7226	0.1495	0.4266	-0.1638	-0.1402	0.1447	-0.0801	0.1734	0.0218	-0.2825	0.3169	0.0074	-0.0845	0.2862	-0.063	0.3436	39.354	-76.0808	85.0623
17	7.5835	1.1148	2.5848	4.4447	1.9014	8.0195	-0.2239	1.5459	-0.2773	-1.2348	0.0417	0.2889	0.0441	0.1143	0.0608	0.9161	-0.1825	-0.2994	1.0533	-0.1028	0.6126	26.3032	-90.6402	58.4466
18	6.4885	3.6797	-0.5962	7.2439	0.7135	3.1577	0.1842	0.1637	-2.1208	0.4159	0.044	-0.8166	0.5347	0.523	-0.3874	0.7958	-0.0699	-0.4119	0.7993	-0.0433	0.805	33.8358	-96.4018	73.613
19	4.4295	-0.7931	-0.9326	2.5182	-0.5326	3.0661	0.4149	0.0714	1.4179	-0.0561	0.0444	-0.4	-0.9318	0.0306	-0.1084	0.4694	0.0148	0.1391	0.1978	-0.0216	0.5728	84.1731	-13.156	104.9894
20	3.7612	2.0048	2.4028	4.1654	-0.7446	5.5215	-0.344	1.5021	0.4889	-0.6603	0.2687	-0.0188	-0.2943	-0.2859	0.1131	0.4355	0.1193	0.0582	0.6066	0.166	0.2319	78.8555	-20.5288	93.1133
21	5.2385	0.5797	-1.1029	4.201	-2.8618	3.4538	-0.1872	0.5887	-0.7889	-0.2647	0.1017	-0.084	0.7391	-0.1708	-0.0023	0.2435	-0.0138	-0.0169	0.1771	-0.049	0.2611	79.8247	-33.8922	102.7071
22	1.7665	0.2039	1.0203	0.6788	0.2208	0.5992	0.0237	0.3519	0.0312	-0.0166	0.0142	0.0495	0.0329	0.0904	-0.0364	0.2559	-0.0007	0.0211	0.2122	0.0422	0.1029	51.5186	-32.2406	100.6593
23	4.387	0.117	-0.553	0.5956	-0.1308	0.0733	-0.0255	-0.1679	0.311	0.0069	0.0491	-0.0226	-0.0586	0.0902	0.0002	0.2648	0.0084	0.02	0.1716	-0.0006	0.0994	62.96	-23.5279	108.088
24	0.8041	-0.4789	-0.7693	1.2752	0.0696	0.8229	0.1909	0.3403	-0.1409	-0.5531	-0.2253	-0.2541	-0.1036	-0.0784	-0.0301	0.4424	0.1206	0.1163	0.6775	-0.0466	0.1481	65.4439	-38.0471	84.1175
25	7.0063	-4.9509	-1.5465	7.7329	2.6192	0.9646	0.0843	1.4901	-1.6899	-0.129	-0.8464	0.2668	0.1585	-0.57	0.8367	0.965	0.0291	0.1563	0.9168	-0.088	0.7284	76.8942	-57.8094	64.5223
26	2.2817	-0.9777	-2.3855	2.36	2.9787	4.4707	0.3033	1.2425	0.5043	-0.6906	-0.3439	0.2772	-0.8939	-1.4637	-0.1422	1.2303	0.418	0.3456	1.4113	0.2293	0.5283	70.3501	-43.638	61.261

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 131 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 132 through 245 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 246 through 1053 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1054 through 1091 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1092 through 1121 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1122 through 1152 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 118 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 119 through 314 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 315 through 1054 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1055 through 1095 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1096 through 1151 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 131 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 132 through 200 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 201 through 314 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 315 through 1053 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1054 through 1110 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 1111 through 1152 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 0 through 42 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 43 through 72 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 73 through 105 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 106 through 200 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 201 through 314 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 315 through 1054 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 1055 through 1110 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1111 through 1152 )

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