PDB-9ku0: Crystal structure of CtpA F105R mutant from Helicobacter pylori

ID or keywords:

Entry

Database: PDB / ID: 9ku0

Title

Crystal structure of CtpA F105R mutant from Helicobacter pylori

Components

Carboxyl-terminal protease

Keywords

HYDROLASE / Carboxyl-terminal processing protease / CtpA

Function / homology

Function and homology information

serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function

Biological species

Helicobacter pylori G27 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.7 Å

Authors

Sun, K. / Au, S.W.N.

Funding support

Hong Kong, 1items

Citation

Journal: To Be Published
Title: Crystal structure of CtpA F105R mutant from Helicobacter pylori
Authors: Sun, K. / Au, S.W.N.

History

Deposition	Dec 3, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ku0.cif.gz	569 KB	Display	PDBx/mmCIF format
PDB format	pdb9ku0.ent.gz	480.3 KB	Display	PDB format
PDBx/mmJSON format	9ku0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ku0_validation.pdf.gz	450.6 KB	Display	wwPDB validaton report
Full document	9ku0_full_validation.pdf.gz	464.7 KB	Display
Data in XML	9ku0_validation.xml.gz	54.6 KB	Display
Data in CIF	9ku0_validation.cif.gz	70.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ku/9ku0 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/9ku0	HTTPS FTP

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Related structure data

Related structure data	9jr1
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

Deposited unit

A: Carboxyl-terminal protease

B: Carboxyl-terminal protease

C: Carboxyl-terminal protease

D: Carboxyl-terminal protease

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

1

A: Carboxyl-terminal protease

B: Carboxyl-terminal protease

defined by author&software
Evidence: electron microscopy
277 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1
crystal symmetry operation	1_565	x,y+1,z	1
crystal symmetry operation	2_445	-y-1,x-y-1,z	1
crystal symmetry operation	3_655	-x+y+1,-x,z	1

2

C: Carboxyl-terminal protease

D: Carboxyl-terminal protease

defined by author&software
Evidence: electron microscopy
277 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_545	-y,x-y-1,z	1
crystal symmetry operation	3_655	-x+y+1,-x,z	1
crystal symmetry operation	4_555	x+2/3,y+1/3,z+1/3	1
crystal symmetry operation	5_445	-y-1/3,x-y-2/3,z+1/3	1
crystal symmetry operation	6_545	-x+y+2/3,-x-2/3,z+1/3	1

Unit cell

Length a, b, c (Å)	139.331, 139.331, 252.092
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Carboxyl-terminal protease Mass: 46128.227 Da / Num. of mol.: 4 / Mutation: F105R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Strain: G27 / Gene: HPG27_1298 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z8Z7
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.81 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-tris (pH 6.5), 100 mM magnesium chloride, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.7→28.01 Å / Num. obs: 19454 / % possible obs: 99.77 % / Redundancy: 5.2 % / R_merge(I) obs: 0.126 / Net I/σ(I): 7.9
Reflection shell	Resolution: 3.7→4.05 Å / R_merge(I) obs: 0.521 / Num. unique obs: 4677

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Processing

Software

Name	Version	Classification
PHENIX	(dev_5526: ???)	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.7→28.01 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3124	1029	5.29 %
R_work	0.2422	-	-
obs	0.246	19443	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.7→28.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11012	0	0	0	11012

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004
X-RAY DIFFRACTION	f_angle_d	0.872
X-RAY DIFFRACTION	f_dihedral_angle_d	12.666	4310
X-RAY DIFFRACTION	f_chiral_restr	0.055	1770
X-RAY DIFFRACTION	f_plane_restr	0.006	1905

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 (%)
3.7-3.89	0.3572	131	0.3314	2660	X-RAY DIFFRACTION	100
3.9-4.14	0.3829	148	0.2889	2644	X-RAY DIFFRACTION	100
4.14-4.46	0.3159	163	0.2596	2594	X-RAY DIFFRACTION	100
4.46-4.9	0.3093	169	0.2448	2595	X-RAY DIFFRACTION	100
4.9-5.61	0.3093	135	0.2612	2650	X-RAY DIFFRACTION	100
5.61-7.04	0.3485	150	0.2713	2611	X-RAY DIFFRACTION	100
7.05-28.01	0.2667	133	0.1838	2660	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	2.9923	1.3992	-1.4853	4.0775	2.2422	3.9966	-1.1183	-2.7455	0.3279	0.5318	0.0486	2.2371	0.0449	-0.6395	0.7967	1.0528	0.0969	0.222	1.5544	0.256	2.9043	-3.0975	-62.6782	20.7464
2	2.8721	-1.4007	-0.8281	0.6122	0.75	3.9347	0.2643	1.5759	-0.5807	-0.919	-0.5048	-0.1888	2.0478	-0.5174	0.0571	2.0077	0.1563	-0.3087	1.3623	-0.1731	1.4204	10.4708	-52.2365	3.1327
3	6.9301	-1.1686	-2.2002	2.7555	1.8664	5.514	-0.3725	-0.5184	-1.4955	-0.3533	0.0484	-0.6114	0.541	-0.6009	0.4191	1.2176	-0.2324	-0.0789	1.2591	0.1623	1.5102	7.7011	-35.3557	7.4963
4	3.3193	-1.6382	0.4976	3.1866	0.0613	0.2703	-0.2648	-0.5901	0.5627	-2.3873	0.056	-0.9918	0.0089	-1.9773	0.159	1.5355	-0.1262	-0.0122	1.9508	0.1366	0.2605	30.1526	-29.1976	0.4389
5	3.3941	-0.1261	-1.129	6.8497	-0.4975	2.0358	-0.3003	0.6219	-0.9101	-0.4134	0.1866	0.0078	0.2037	0.2092	0.0569	0.8418	0.0399	0.0163	1.1146	-0.1366	0.57	35.686	-38.4477	11.1826
6	2.1244	-1.5785	1.1296	3.8168	0.7024	1.7055	-0.6051	0.4995	-1.0314	-1.4833	-0.532	0.1157	-0.9995	0.1579	0.8299	1.5453	-0.6357	0.0534	1.2056	0.0899	0.9866	21.0528	-53.2389	14.3984
7	6.839	-1.4903	-0.9587	1.8189	-1.2797	1.0799	-0.7962	-0.1331	2.9986	-0.8807	0.8848	0.2336	-0.2028	-0.7612	-0.0887	1.3015	-0.2259	-0.3041	0.9517	0.1928	1.2621	32.6993	-19.2383	14.6731
8	3.4111	3.7685	0.322	5.8544	2.7112	3.7197	-0.2629	0.5349	2.6098	-0.1649	0.0417	1.2254	-0.2823	0.0161	0.3505	1.0108	0.2657	0.1502	1.1042	0.1786	2.1294	10.526	-97.3069	20.8564
9	3.1975	-2.4627	-2.8843	3.6506	2.9326	2.8834	-0.8638	-1.1982	0.9503	0.7436	0.1281	-0.5733	1.5077	-0.7816	0.7663	1.5121	-0.0457	0.1577	1.7678	-0.2314	1.4739	26.4436	-90.8859	36.0471
10	7.6533	-4.2972	2.2858	4.3403	1.6432	9.7909	0.2789	-0.3076	-2.3908	0.281	-0.2565	1.0831	0.9518	-0.9565	-0.1564	1.1315	-0.1971	-0.1669	0.9845	-0.0043	1.9436	40.9038	-100.3829	32.4973
11	6.5798	-2.2872	0.4672	2.8849	0.4485	2.8096	0.1236	0.4434	-0.1958	0.5348	-0.1277	0.1902	-0.0224	0.0397	0.0518	0.9243	-0.1277	0.0986	0.5582	-0.0337	0.499	52.7662	-78.9842	29.4397
12	4.9917	2.8236	4.0962	3.5137	5.5647	8.6535	-0.014	0.4925	-0.3303	-0.3197	-1.058	1.3332	-0.5146	0.0641	1.043	0.9577	0.093	0.1126	1.0344	0.1135	1.5156	12.601	-11.8464	61.7643
13	7.4933	0.3805	-1.5534	2.8254	1.0033	2.2705	0.3675	-0.8694	0.7579	0.6331	-0.127	0.6796	0.1004	-0.0756	-0.2838	1.4012	-0.0766	-0.1829	1.0338	-0.038	0.9584	24.3151	-33.962	48.0005
14	6.4174	1.9845	-1.1956	6.7495	2.0464	6.3057	0.2047	-0.5926	-0.3784	0.5124	0.1003	0.9271	-0.2636	0.0514	-0.1663	1.0114	0.2293	0.2617	0.7798	0.1764	0.8539	35.6821	-30.3078	50.5011
15	1.9594	1.7599	-0.655	1.791	-0.7838	0.2294	1.2062	0.6541	0.475	-0.2993	-1.4223	-0.28	-0.2845	1.1026	0.2966	1.7765	0.2244	0.0652	1.4923	-0.0411	0.6236	32.4897	-56.5684	43.1683
16	4.5285	-2.6016	-4.3945	6.5725	0.5412	5.5536	0.5072	0.4137	-0.5067	-1.6403	-0.6084	1.2736	0.6609	-0.8419	-0.0162	1.3056	-0.1407	-0.3291	0.8669	0.0677	0.7383	19.9259	-58.0739	51.2417
17	2.7269	-3.4389	3.6782	5.5478	-2.1821	6.9097	0.3305	-0.8888	0.3591	-0.3889	-0.4368	1.5619	-0.3581	-1.1357	-0.0066	0.8125	-0.0041	0.0002	1.1029	-0.0387	1.2792	19.895	-46.7202	56.4305
18	-0.2306	-0.0379	-0.2835	5.8899	0.8037	5.6827	0.2363	0.911	-0.1483	0.2565	-0.2436	-0.2944	0.1156	0.0968	0.1257	0.8738	0.1405	0.0222	0.8931	0.0234	0.8775	33.2988	-57.4955	57.163
19	4.0198	-3.1153	0.8176	4.4378	-4.4922	6.6757	-0.5356	0.4345	-0.7792	0.6968	0.5267	-0.4815	-0.5474	0.2789	-0.2776	1.4334	-0.2579	0.1993	1.2501	-0.3697	1.9049	44.6811	-35.3827	-21.4973
20	0.5323	1.1854	1.4675	2.2195	1.9978	7.4435	0.3701	-0.6045	0.5602	1.0427	1.02	-1.906	-0.3279	1.4883	-1.3678	1.7028	0.397	-0.0165	1.7826	-0.6598	1.7315	46.6443	-52.4378	-4.8596
21	7.324	-2.0412	-2.1582	3.9569	0.4553	8.3864	-0.271	0.8816	0.6005	-0.228	0.5285	-0.4108	0.0259	1.1538	-0.103	0.9472	-0.1694	-0.0125	1.5163	-0.2459	1.0436	31.685	-61.6747	-7.9131
22	6.6366	-3.3008	-2.0984	9.4685	-2.0137	4.9716	0.4054	-0.086	-1.2026	-0.8775	0.4585	-0.7089	0.071	-0.7337	-1.3672	1.0944	-0.096	-0.1113	1.0224	0.1141	0.7804	41.6778	-82.4064	-1.9762
23	5.4471	2.2066	-0.2624	7.8293	-2.0985	3.2373	0.4985	-0.7997	0.1338	0.1705	-0.0926	-0.96	0.2849	0.5699	-0.3679	0.6414	-0.0547	-0.0617	1.2222	-0.1471	0.9311	53.2161	-80.8869	-11.8255
24	0.7211	1.4386	-0.1675	4.6474	2.6033	3.4191	-0.2022	-0.817	0.5134	0.0029	-0.0496	0.872	0.0706	0.0751	0.2574	0.685	0.0421	-0.0915	0.9697	-0.0773	1.2403	43.3924	-78.9887	-17.2089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 45 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 109 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 110 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 217 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 218 through 326 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 327 through 356 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 357 through 445 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 80 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 81 through 109 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 110 through 188 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 189 through 445 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 45 through 80 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 81 through 133 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 134 through 188 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 189 through 217 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 218 through 300 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 301 through 339 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 340 through 445 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 45 through 80 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 81 through 109 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 110 through 187 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 188 through 217 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 218 through 311 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 312 through 445 )

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