PDB-4tsd: Crystal structure of Helicobacter pylori HP1029

ID or keywords:

Entry

Database: PDB / ID: 4tsd

Title

Crystal structure of Helicobacter pylori HP1029

Components

HP1029

Keywords

UNKNOWN FUNCTION / Pfam Family PF04074 / Zinc binding

Function / homology

NanQ anomerase/TabA/YiaL family / NanQ anomerase/TabA/YiaL superfamily / YhcH/YjgK/YiaL / metal ion binding / cytosol / Flagellar motor switch protein

Function and homology information

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Vallese, F. / Percudani, R. / Zanotti, G.

Funding support

Italy, 2items

Citation

Journal: Febs J. / Year: 2015
Title: The crystal structure of Helicobacter pylori HP1029 highlights the functional diversity of the sialic acid-related DUF386 family.
Authors: Vallese, F. / Percudani, R. / Fischer, W. / Zanotti, G.

History

Deposition	Jun 18, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 10, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 17, 2015	Group: Database references
Revision 1.2	Jul 8, 2015	Group: Database references
Revision 1.3	Sep 9, 2015	Group: Database references
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tsd.cif.gz	169.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4tsd.ent.gz	133.4 KB	Display	PDB format
PDBx/mmJSON format	4tsd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/4tsd ftp://data.pdbj.org/pub/pdb/validation_reports/ts/4tsd	HTTPS FTP

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Related structure data

Related structure data	1s4cS 4tsz S: Starting model for refinement
Similar structure data	7cel-d 6grn-d 4c4d-d 3crb-d 5d56-1 5t0n-4 1egn-d 4xeb-d 4uwt-d 1u7c-d 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

B: HP1029

A: HP1029

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.788, 77.490, 99.134
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HP1029 Mass: 22376.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: C694_05325, HP_1029 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25673
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Tris, 8% w/v PEG 8000 (solution number 38 SS1 kit, Molecular Dimensions) PH range: 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.28167 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28167 Å / Relative weight: 1
Reflection	Resolution: 1.53→49.57 Å / Num. all: 50272 / Num. obs: 50272 / % possible obs: 95 % / Redundancy: 11 % / R_merge(I) obs: 0.056 / Net I/σ(I): 27.1
Reflection shell	Resolution: 1.53→1.58 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.704 / Mean I/σ(I) obs: 2 / % possible all: 68.2

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
SCALA		data scaling
MOLREP		phasing
Coot		model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1S4C

1s4c

Resolution: 1.53→49.567 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1849	4918	5.15 %	Random Selection
R_work	0.1578	-	-	-
obs	0.1592	50203	95.01 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→49.567 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2882	0	6	373	3261

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2965
X-RAY DIFFRACTION	f_angle_d	1.102	3980
X-RAY DIFFRACTION	f_dihedral_angle_d	12.855	1109
X-RAY DIFFRACTION	f_chiral_restr	0.056	428
X-RAY DIFFRACTION	f_plane_restr	0.005	510

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 (%)
1.53-1.5474	0.2997	118	0.2544	1901	X-RAY DIFFRACTION	60
1.5474-1.5656	0.2451	92	0.2447	2202	X-RAY DIFFRACTION	69
1.5656-1.5847	0.2585	123	0.2248	2437	X-RAY DIFFRACTION	76
1.5847-1.6048	0.281	151	0.2285	2562	X-RAY DIFFRACTION	80
1.6048-1.6259	0.2159	163	0.2017	2744	X-RAY DIFFRACTION	86
1.6259-1.6482	0.2175	179	0.1887	2838	X-RAY DIFFRACTION	90
1.6482-1.6717	0.2091	155	0.1835	2917	X-RAY DIFFRACTION	94
1.6717-1.6967	0.1923	156	0.1807	3109	X-RAY DIFFRACTION	97
1.6967-1.7232	0.1936	159	0.1794	3226	X-RAY DIFFRACTION	99
1.7232-1.7514	0.1956	179	0.1704	3120	X-RAY DIFFRACTION	100
1.7514-1.7816	0.2108	169	0.1671	3185	X-RAY DIFFRACTION	100
1.7816-1.814	0.2183	203	0.1675	3118	X-RAY DIFFRACTION	100
1.814-1.8489	0.2259	159	0.17	3210	X-RAY DIFFRACTION	100
1.8489-1.8867	0.1686	174	0.1529	3147	X-RAY DIFFRACTION	100
1.8867-1.9277	0.1858	176	0.1627	3191	X-RAY DIFFRACTION	100
1.9277-1.9725	0.2076	169	0.1593	3216	X-RAY DIFFRACTION	100
1.9725-2.0218	0.1981	172	0.1557	3186	X-RAY DIFFRACTION	100
2.0218-2.0765	0.1771	169	0.1503	3151	X-RAY DIFFRACTION	100
2.0765-2.1376	0.1721	174	0.163	3204	X-RAY DIFFRACTION	100
2.1376-2.2066	0.2059	210	0.1593	3136	X-RAY DIFFRACTION	100
2.2066-2.2855	0.179	169	0.158	3176	X-RAY DIFFRACTION	100
2.2855-2.377	0.1696	189	0.1605	3198	X-RAY DIFFRACTION	100
2.377-2.4852	0.1611	167	0.1595	3190	X-RAY DIFFRACTION	100
2.4852-2.6162	0.1944	134	0.1603	3192	X-RAY DIFFRACTION	100
2.6162-2.7801	0.191	169	0.1651	3193	X-RAY DIFFRACTION	100
2.7801-2.9947	0.1835	163	0.1699	3182	X-RAY DIFFRACTION	100
2.9947-3.296	0.201	180	0.1604	3179	X-RAY DIFFRACTION	100
3.296-3.7728	0.1636	156	0.1418	3181	X-RAY DIFFRACTION	100
3.7728-4.7528	0.1429	153	0.1312	3216	X-RAY DIFFRACTION	100
4.7528-49.593	0.1909	188	0.1504	3150	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	3.5105	-0.7331	-3.0848	4.9801	1.2685	3.8863	0.1855	-0.5404	0.3357	-0.0923	0.0369	-0.3072	-0.0974	0.5392	-0.2186	0.1749	-0.0336	-0.0236	0.2427	-0.0035	0.1829	4.5697	-9.6601	19.5058
2	6.548	-4.5984	1.2536	6.9852	-1.2627	4.5692	0.1618	0.0392	0.318	-0.4694	-0.0021	-0.5684	-0.2348	0.5594	-0.0733	0.168	-0.054	0.0664	0.2383	-0.0054	0.2286	8.3349	-9.3469	9.4517
3	2.2755	-1.6699	0.0542	4.0525	-1.0821	2.9366	0.2406	0.2667	0.2456	-0.4902	-0.1387	-0.2625	-0.4046	-0.0009	-0.0868	0.3551	0.0077	0.0804	0.2231	0.0429	0.1697	-0.7482	-4.5769	-0.4522
4	2.7206	-0.5182	0.0774	2.4227	-0.1542	2.0352	0.0608	0.0484	0.1197	-0.2312	0.0161	0.2714	-0.0589	-0.2727	-0.088	0.1958	0.026	-0.0347	0.1897	0.0101	0.1909	-12.4901	-10.9378	7.5027
5	2.0891	0.1907	-0.0896	3.2876	0.4574	1.5591	0.1096	0.0069	-0.0419	-0.0385	-0.0865	-0.011	-0.0001	-0.1272	-0.0111	0.115	-0.0018	-0.02	0.1038	0.0127	0.0841	-8.903	-15.3876	13.1477
6	2.486	1.6834	-3.5423	4.463	-1.1957	9.3015	0.0863	0.3003	-0.1496	-0.3981	-0.0611	0.1767	0.4596	-0.2675	0.0037	0.2354	-0.0178	-0.0767	0.1834	-0.0188	0.1943	-13.1716	-27.569	7.4333
7	1.8288	0.613	0.3676	3.8912	0.6681	2.241	0.0733	-0.0521	0.0157	-0.0231	-0.0635	0.168	-0.0305	-0.1831	-0.0061	0.132	0.0067	-0.0058	0.1361	0.0123	0.1075	-12.3241	-12.8698	15.7298
8	6.1573	0.5219	1.2602	9.1114	-1.3356	6.8047	0.265	0.1281	0.733	-0.2198	0.0058	0.7376	-0.6906	-1.1011	-0.2752	0.3201	0.1331	-0.0171	0.3068	0.0386	0.3525	-17.9311	2.1769	9.6184
9	1.5214	0.4407	-0.4597	1.428	1.0007	1.236	0.0543	-0.3409	-0.1603	-0.0066	0.0649	-0.1929	0.1878	0.0748	-0.1527	0.1407	0.0127	0.009	0.1939	0.0322	0.1563	2.0834	-17.0404	15.1563
10	3.8366	0.2603	1.3488	2.8732	-0.0227	3.2018	0.0856	0.0857	-0.4521	-0.0817	-0.0253	-0.3958	0.4739	0.5701	-0.0443	0.2364	0.0575	0.0317	0.248	-0.015	0.2357	0.3766	-22.645	29.6298
11	8.2574	4.0835	-0.9719	6.895	0.1081	2.2126	-0.3201	0.2332	-0.6728	0.0609	0.3307	-0.571	0.8264	0.393	-0.0221	0.2855	0.0193	0.0104	0.2501	-0.0345	0.2347	-2.5689	-25.8213	39.0457
12	7.0244	0.9017	-1.1361	3.505	2.5128	2.2694	-0.5137	-0.1876	-0.9266	0.1501	0.2211	0.0413	0.8901	-0.1375	0.174	0.2618	-0.0366	0.0879	0.205	0.0573	0.2743	-11.9284	-26.9632	45.418
13	8.4783	-1.9382	-1.576	1.3791	0.5382	1.6784	0.0775	-0.3636	0.2216	0.1089	0.0105	-0.0927	-0.1775	0.0802	-0.0755	0.1517	0.0046	0.0084	0.1995	0.0347	0.1267	-8.6765	-15.9734	48.6945
14	2.9808	-0.8487	0.351	2.3305	-1.0963	2.9602	0.0684	0.1631	0.2114	0.0401	0.0101	0.2474	-0.3162	-0.2179	-0.0732	0.1266	0.0083	0.0042	0.1594	0.0169	0.167	-12.317	-7.9434	38.6592
15	2.7298	0.5308	0.3482	2.2656	-0.1647	2.5367	-0.0191	-0.0184	0.0767	0.0189	-0.0184	-0.0519	-0.234	0.0036	0.0296	0.1065	-0.0143	-0.0013	0.0964	0.0016	0.1073	-6.3404	-7.9618	33.5553
16	6.2298	-3.2692	3.8201	3.2234	-3.2087	3.8175	-0.2548	-0.353	0.4409	0.446	-0.0557	-0.2531	-0.8521	0.0545	0.2499	0.3908	-0.0843	-0.037	0.2267	-0.0269	0.2332	-0.5934	3.2127	39.5627
17	2.2408	0.695	-0.2953	3.1823	-0.1756	3.1265	0.0003	0.0378	0.0998	-0.0961	0.0385	0.0683	-0.2204	-0.2019	-0.0313	0.1148	-0.0008	-0.0138	0.1309	0.0096	0.1092	-10.2576	-7.0101	30.6317
18	4.1054	0.4711	0.4062	5.9904	-1.078	5.5847	-0.0902	-0.0416	0.1904	-0.084	0.4708	0.9913	-0.2764	-0.9679	-0.1911	0.1342	0.002	-0.0285	0.4922	0.0827	0.3764	-25.5395	-12.2977	36.1271
19	0.1706	0.1609	0.4122	1.1948	-0.4407	1.959	-0.0235	0.085	0.1409	-0.1243	-0.0212	-0.1652	0.0583	0.3623	0.0174	0.1262	-0.0057	-0.0008	0.2002	0.0374	0.1679	1.1802	-14.7833	33.7669

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 18 through 31 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 32 through 55 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 56 through 77 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 78 through 104 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 105 through 117 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 118 through 151 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 152 through 161 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 162 through 182 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 2 through 20 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 21 through 31 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 32 through 42 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 43 through 55 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 56 through 77 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 78 through 104 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 105 through 117 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 118 through 151 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 152 through 161 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 162 through 180 )

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