PDB-8dol: Mechanism of regulation of the Helicobacter pylori Cagbeta ATPase...

ID or keywords:

Entry

Database: PDB / ID: 8dol

Title

Mechanism of regulation of the Helicobacter pylori Cagbeta ATPase by CagZ

Components

Cag pathogenicity island protein (Cag5)

Keywords

TRANSPORT PROTEIN / type IV secretion system / Cagbeta coupling ATPase / CagZ

Function / homology

Type IV secretion system protein TraG/VirD4 / Type IV secretory system Conjugative DNA transfer / : / P-loop containing nucleoside triphosphate hydrolase / plasma membrane / DI(HYDROXYETHYL)ETHER / Cag pathogenicity island protein (Cag5)

Function and homology information

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Wu, X. / Zhao, Y. / Yang, W. / Sun, L. / Ye, X. / Jiang, M. / Wang, Q. / Wang, Q. / Zhang, X. / Wu, Y.

Funding support

United States,

China, 6items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R35GM130289	United States
Welch Foundation	I-1702	United States
Other government	2017N0031
Other government	2016T3041
Other government	31470741
Other government	2017L3009	China

Citation

Journal: Nat Commun / Year: 2023
Title: Mechanism of regulation of the Helicobacter pylori Cag beta ATPase by CagZ.
Authors: Wu, X. / Zhao, Y. / Zhang, H. / Yang, W. / Yang, J. / Sun, L. / Jiang, M. / Wang, Q. / Wang, Q. / Ye, X. / Zhang, X. / Wu, Y.

History

Deposition	Jul 13, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	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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PDBx/mmCIF format	8dol.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8dol.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	8dol.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8dol_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8dol_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8dol_validation.xml.gz	105.8 KB	Display
Data in CIF	8dol_validation.cif.gz	141 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/do/8dol ftp://data.pdbj.org/pub/pdb/validation_reports/do/8dol	HTTPS FTP

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Related structure data

Related structure data	6jho
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	#211 - Jul 2017 Pilus Machine similarity (1)

Deposited unit

A: Cag pathogenicity island protein (Cag5)

B: Cag pathogenicity island protein (Cag5)

C: Cag pathogenicity island protein (Cag5)

D: Cag pathogenicity island protein (Cag5)

E: Cag pathogenicity island protein (Cag5)

F: Cag pathogenicity island protein (Cag5)

hetero molecules

404 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, high oligomer appeared

Unit cell

Length a, b, c (Å)	112.115, 163.277, 112.220
Angle α, β, γ (deg.)	90.000, 93.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cag pathogenicity island protein (Cag5) Mass: 67193.828 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0524 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25260
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.54 Å³/Da / Density % sol: 51.64 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / Details: 35% PEG400, 0.2 M Li2SO4, 0.1 M Tris 8.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: AichiSR

/ Beamline: BL2S1 / Wavelength: 0.979183 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.979183 Å / Relative weight: 1

Reflection

Resolution: 2.8→50 Å / Num. obs: 97939 / % possible obs: 100 % / Redundancy: 6.8 % / B_iso Wilson estimate: 77.39 Å² / R_merge(I) obs: 0.073 / R_pim(I) all: 0.03 / R_rim(I) all: 0.079 / Χ²: 0.679 / Net I/σ(I): 7.8 / Num. measured all: 669386

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.8-2.85	7.1	0.95	4866	0.752	0.384	1.026	0.421	100
2.85-2.9	7	0.837	4867	0.807	0.34	0.904	0.431	100
2.9-2.96	6.9	0.665	4870	0.848	0.272	0.719	0.432	100
2.96-3.02	6.8	0.539	4916	0.899	0.222	0.583	0.442	100
3.02-3.08	6.6	0.429	4852	0.931	0.181	0.466	0.45	100
3.08-3.15	6.5	0.368	4875	0.935	0.155	0.4	0.464	100
3.15-3.23	7.1	0.303	4866	0.965	0.122	0.327	0.471	100
3.23-3.32	7.1	0.237	4889	0.977	0.096	0.256	0.493	100
3.32-3.42	7	0.183	4923	0.987	0.074	0.198	0.509	100
3.42-3.53	7	0.143	4884	0.991	0.058	0.154	0.587	100
3.53-3.65	6.8	0.112	4919	0.994	0.047	0.122	0.619	100
3.65-3.8	6.5	0.095	4850	0.995	0.04	0.103	0.67	100
3.8-3.97	7	0.079	4880	0.996	0.032	0.085	0.75	100
3.97-4.18	7	0.064	4944	0.998	0.026	0.069	0.819	100
4.18-4.44	6.9	0.053	4883	0.998	0.022	0.058	0.906	100
4.44-4.79	6.5	0.048	4921	0.998	0.02	0.052	1.004	100
4.79-5.27	7	0.045	4888	0.998	0.018	0.048	0.987	100
5.27-6.03	7	0.046	4921	0.998	0.019	0.049	0.948	100
6.03-7.59	6.7	0.041	4945	0.998	0.017	0.044	1.008	100
7.59-50	6.3	0.033	4980	0.998	0.015	0.036	1.229	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-3000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold AF-O25260-F1

Resolution: 2.8→40.79 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2469	1986	2.03 %
R_work	0.197	95799	-
obs	0.198	97785	99.23 %

Solvent computation

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

Displacement parameters

B_iso max: 306.51 Å² / B_iso mean: 99.3862 Å² / B_iso min: 32.47 Å²

Refinement step

Cycle: final / Resolution: 2.8→40.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24484	0	72	11	24567
B_iso mean	-	-	89.95	51.9	-
Num. residues	-	-	-	-	3145

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8-2.87	0.317	150	0.2699	6240	6390	91
2.87-2.95	0.2945	121	0.2593	6924	7045	100
2.95-3.04	0.3145	135	0.2571	6833	6968	100
3.04-3.14	0.3245	150	0.2583	6871	7021	100
3.14-3.25	0.2978	132	0.2499	6877	7009	100
3.25-3.38	0.3363	138	0.2409	6908	7046	100
3.38-3.53	0.2965	140	0.222	6839	6979	100
3.53-3.72	0.2764	160	0.2104	6914	7074	100
3.72-3.95	0.2248	134	0.1852	6865	6999	100
3.95-4.26	0.2192	144	0.1708	6903	7047	100
4.26-4.68	0.2111	131	0.1589	6964	7095	100
4.68-5.36	0.2066	149	0.1709	6889	7038	100
5.36-6.75	0.3225	146	0.2131	6909	7055	100
6.75-40.79	0.1912	156	0.1808	6863	7019	98

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	2.336	-1.256	0.8041	4.3346	-3.0914	4.4177	0.0614	0.2887	-0.1688	-0.698	-0.0175	0.1332	0.5991	-0.2369	-0.03	0.4264	-0.041	-0.0191	0.4098	-0.0745	0.3309	11.8321	-19.9594	48.4747
2	1.6787	-1.9078	-0.6582	7.1542	1.7139	2.2371	0.0759	-0.031	0.4449	0.026	-0.0439	0.0797	-0.5413	-0.373	-0.0377	0.5474	0.0929	-0.0141	0.5007	0.0843	0.5665	2.2096	19.205	53.5145
3	1.3146	-0.937	0.8733	2.4331	-0.9679	1.668	-0.0185	0.2549	0.1203	-0.3954	-0.08	-0.0971	0.1429	-0.0122	0.1133	0.3677	-0.0554	0.0252	0.4396	-0.0304	0.3708	18.1644	-17.4361	53.4117
4	6.464	-3.7007	0.345	3.9155	0.0282	1.3282	-0.0134	0.4711	-0.3075	0.1088	-0.0708	0.5746	0.2026	-0.5978	0.0416	0.3695	-0.1605	0.0607	0.735	-0.0397	0.5021	-10.3251	-21.1778	79.6237
5	2.975	4.0932	0.5185	7.216	2.0481	4.2589	0.1299	-0.1154	1.1432	1.051	-0.4558	-0.7733	-0.9503	0.3139	0.1302	0.9891	0.0707	-0.3261	0.9382	0.218	1.7412	-7.1338	11.9203	85.289
6	3.3445	-0.9266	0.6769	3.3648	0.678	3.2339	-0.4138	0.2029	1.4633	-0.0987	-0.0243	-0.2055	-1.1555	-0.0844	0.2463	0.7061	0.0001	-0.2252	0.594	0.0949	1.1367	-8.46	7.6014	84.5426
7	2.3843	-0.6466	-0.3369	1.3047	0.4147	0.9222	-0.0133	0.5887	0.0074	-0.2667	-0.1935	0.2001	0.1759	-0.3742	0.193	0.4504	-0.1033	0.0218	0.6794	0.0013	0.4697	-0.1034	-26.336	73.2258
8	4.2947	-0.5729	-1.8504	3.7159	1.4444	6.7117	-0.4576	-0.4879	-0.163	0.7546	0.1561	0.7046	0.1478	-0.8418	0.2695	0.5273	-0.0084	0.14	0.6164	0.0226	0.5432	5.7253	-20.5946	115.3694
9	1.059	1.1107	1.8264	2.2284	0.1638	1.7265	-0.1649	0.3157	0.6779	-0.3774	-0.291	0.0791	-1.9483	-0.2205	0.339	2.4959	0.5333	0.0174	0.9725	-0.024	1.8754	4.2901	22.7718	116.3799
10	1.167	-0.2815	-0.0879	2.6085	0.9786	4.1394	-0.1854	-0.1036	0.0479	0.076	-0.1108	0.5233	-0.5553	-0.9699	0.2082	0.4772	0.069	0.0023	0.674	0.0627	0.5273	6.0057	-14.8985	107.7849
11	1.9167	0.709	-0.6041	3.2993	1.285	3.7098	0.1669	-0.687	0.3497	0.6281	0.1835	-0.2467	-0.3281	0.9837	-0.2194	0.5049	-0.0498	-0.0105	0.8293	-0.1501	0.4575	43.6788	-4.0999	115.4006
12	1.5465	1.1599	0.7219	6.1943	-2.9752	4.7061	-0.1133	0.1267	0.8174	0.2641	-0.1564	0.8011	-1.4632	0.4955	0.1941	1.6849	-0.1736	0.1724	0.8132	-0.0895	1.4237	36.5537	33.4886	102.5822
13	1.5407	0.2198	-0.3138	3.9978	0.8746	2.323	-0.0389	-0.4647	0.3245	0.3317	0.1423	0.2286	-0.2358	0.351	-0.0859	0.405	0.0367	0.0155	0.624	-0.0622	0.381	38.0744	-9.2679	111.1881
14	1.7712	1.7614	0.1592	5.3242	0.5302	1.7084	-0.1292	-0.0213	-0.0877	-0.2711	0.1248	-0.3978	-0.2195	0.0606	-0.0193	0.2894	0.1029	-0.018	0.629	-0.0793	0.4661	67.0589	-3.5144	85.3859
15	1.2022	-0.1157	0.0231	7.6795	-0.1538	1.6061	-0.153	0.2309	0.7108	-0.6277	-0.1142	0.7459	-1.2001	-0.3611	0.1836	1.1199	0.1784	-0.2656	0.6994	-0.0753	0.9174	61.1187	30.8702	82.6688
16	1.4169	0.9295	-0.1918	2.9487	0.0349	0.7645	-0.0343	-0.1632	0.0565	0.0637	-0.041	-0.1172	0.0258	0.1538	0.0818	0.3345	0.1023	0.0277	0.5755	-0.0303	0.3557	59.1506	-11.842	89.109
17	2.9003	1.0617	-0.5259	4.7672	-1.5953	2.9957	-0.1353	0.8191	0.0846	-0.7515	-0.1704	-0.5292	-0.0952	0.5745	0.3296	0.6639	-0.0241	0.0872	0.9255	0.1089	0.4161	50.7903	-10.1237	50.068
18	3.3521	-2.5579	0.089	6.0555	1.9816	1.2311	-0.159	0.4016	1.2775	-1.117	-0.6792	0.6408	-1.4366	-0.4516	0.6488	1.8189	0.1244	-0.2873	0.9128	0.1636	1.9379	34.2944	30.7624	49.7755
19	1.5565	-0.2911	0.3956	2.7666	-0.6004	2.3112	-0.1881	0.5156	0.2786	-0.2134	-0.076	-0.4406	-0.4184	0.5674	0.2075	0.4803	-0.1001	-0.0067	0.714	0.0562	0.4649	48.3313	-8.3338	57.188

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 181 through 279 )	A	181 - 279
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 280 through 531 )	A	280 - 531
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 532 through 747 )	A	532 - 747
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 181 through 289 )	B	181 - 289
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 290 through 359 )	B	290 - 359
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 360 through 594 )	B	360 - 594
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 595 through 745 )	B	595 - 745
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 180 through 289 )	C	180 - 289
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 290 through 464 )	C	290 - 464
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 465 through 742 )	C	465 - 742
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 181 through 347 )	D	181 - 347
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 348 through 488 )	D	348 - 488
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 489 through 747 )	D	489 - 747
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 181 through 347 )	E	181 - 347
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 348 through 531 )	E	348 - 531
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 532 through 747 )	E	532 - 747
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 181 through 299 )	F	181 - 299
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 300 through 479 )	F	300 - 479
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 480 through 747 )	F	480 - 747

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