PDB-6hv1: The apo structure of Dps from Listeria innocua before soaking exp...

ID or keywords:

Entry

Database: PDB / ID: 6hv1

Title

The apo structure of Dps from Listeria innocua before soaking experiments with Zn, Co and La

Components

DNA protection during starvation protein

Keywords

METAL BINDING PROTEIN / Dps / metal binding. cage shaped protein / ferroxidase / itron translocation

Function / homology

Function and homology information

Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function

Biological species

Listeria innocua (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.547 Å

Authors

Zeth, K. / Okuda, M.

Citation

Journal: Inorg.Chem. / Year: 2019
Title: Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.
Authors: Zeth, K. / Sancho-Vaello, E. / Okuda, M.

History

Deposition	Oct 10, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Sep 11, 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 1.3	Sep 18, 2019	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / struct_ref / struct_ref_seq Item: _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code ..._entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.4	Dec 16, 2020	Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.pdbx_collection_date / _struct.title
Revision 1.5	May 15, 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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Validation report

Summary document	6hv1_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	6hv1_full_validation.pdf.gz	468.5 KB	Display
Data in XML	6hv1_validation.xml.gz	30.5 KB	Display
Data in CIF	6hv1_validation.cif.gz	41.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hv/6hv1 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/6hv1	HTTPS FTP

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Related structure data

Related structure data	6huiC 6hvqC 6hx2C 6sevC C: citing same article (ref.)
Similar structure data	2bk6-1 2iy4-2 1qgh-d 2bkc-2 6sev-1 6hx2-1 2iy4-1 2bkc-1 6hvq-1 2xkq-d 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
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (3) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: DNA protection during starvation protein

B: DNA protection during starvation protein

C: DNA protection during starvation protein

D: DNA protection during starvation protein

E: DNA protection during starvation protein

F: DNA protection during starvation protein

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

1

A: DNA protection during starvation protein

B: DNA protection during starvation protein

C: DNA protection during starvation protein

D: DNA protection during starvation protein

E: DNA protection during starvation protein

F: DNA protection during starvation protein

A: DNA protection during starvation protein

B: DNA protection during starvation protein

C: DNA protection during starvation protein

D: DNA protection during starvation protein

E: DNA protection during starvation protein

F: DNA protection during starvation protein

defined by author&software
Evidence: gel filtration
217 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.710, 84.710, 263.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	DNA protection during starvation protein / Ferritin-like protein / Non-heme iron-containing ferritin Mass: 18070.553 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Gene: dps, flp, fri, lin0942 / Production host: Escherichia coli (E. coli) References: UniProt: P80725, Oxidoreductases; Oxidizing metal ions
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

DNA protection during starvation protein / Ferritin-like protein / Non-heme iron-containing ferritin

Mass: 18070.553 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Listeria innocua (bacteria) / Gene: dps, flp, fri, lin0942 / Production host:

Escherichia coli (E. coli)
References: UniProt: P80725, Oxidoreductases; Oxidizing metal ions

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, pH 7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.547→44.761 Å / Num. obs: 59885 / % possible obs: 99.9 % / Redundancy: 4.5 % / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.547→2.61 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Resolution: 2.547→44.761 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 26.65

	R_factor	Num. reflection	% reflection
R_free	0.2273	2994	5 %
R_work	0.1902	-	-
obs	0.1921	59880	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.547→44.761 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7317	0	0	15	7332

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7492
X-RAY DIFFRACTION	f_angle_d	0.796	10107
X-RAY DIFFRACTION	f_dihedral_angle_d	11.323	4477
X-RAY DIFFRACTION	f_chiral_restr	0.047	1098
X-RAY DIFFRACTION	f_plane_restr	0.005	1305

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 (%)
2.547-2.5887	0.4083	141	0.3731	2659	X-RAY DIFFRACTION	98
2.5887-2.6334	0.316	143	0.3509	2746	X-RAY DIFFRACTION	100
2.6334-2.6812	0.3688	147	0.3196	2687	X-RAY DIFFRACTION	100
2.6812-2.7328	0.3477	145	0.316	2730	X-RAY DIFFRACTION	100
2.7328-2.7886	0.3379	144	0.3101	2674	X-RAY DIFFRACTION	100
2.7886-2.8492	0.3022	139	0.3041	2735	X-RAY DIFFRACTION	100
2.8492-2.9155	0.3374	148	0.3014	2739	X-RAY DIFFRACTION	100
2.9155-2.9884	0.3676	133	0.295	2661	X-RAY DIFFRACTION	100
2.9884-3.0692	0.2939	143	0.2881	2713	X-RAY DIFFRACTION	100
3.0692-3.1594	0.2739	142	0.2668	2727	X-RAY DIFFRACTION	100
3.1594-3.2614	0.2918	147	0.2388	2715	X-RAY DIFFRACTION	100
3.2614-3.3779	0.293	137	0.2375	2719	X-RAY DIFFRACTION	100
3.3779-3.5131	0.2704	142	0.207	2709	X-RAY DIFFRACTION	100
3.5131-3.6729	0.2422	143	0.2081	2700	X-RAY DIFFRACTION	100
3.6729-3.8665	0.2283	143	0.1881	2734	X-RAY DIFFRACTION	100
3.8665-4.1086	0.2094	142	0.1545	2686	X-RAY DIFFRACTION	100
4.1086-4.4255	0.1627	143	0.1334	2715	X-RAY DIFFRACTION	100
4.4255-4.8704	0.1456	142	0.1217	2700	X-RAY DIFFRACTION	100
4.8704-5.574	0.1919	152	0.149	2711	X-RAY DIFFRACTION	100
5.574-7.0183	0.2344	141	0.1849	2720	X-RAY DIFFRACTION	100
7.0183-44.7676	0.1842	137	0.1484	2706	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	1.6046	0.0576	-0.0474	1.1128	-0.3068	2.84	-0.4341	-0.9537	0.0005	0.771	0.3553	-0.4206	0.4583	0.6103	0.0778	0.7348	0.3139	-0.2382	1.0745	0.0228	0.6299	26.4131	-7.8332	20.4673
2	3.04	-3.5813	-3.7185	5.6872	3.949	4.9069	-0.7181	-0.6822	-0.3162	-0.0299	0.3154	0.6791	-0.3941	0.8359	0.4298	0.6219	0.1785	-0.2061	0.8568	0.0272	0.6192	21.4683	-4.9532	13.9927
3	1.097	0.106	0.0161	2.08	0.0386	2.4595	-0.4094	-0.82	0.1974	0.6672	0.2784	-0.783	0.36	0.8574	0.0822	0.6092	0.251	-0.2782	1.2083	-0.0371	0.8663	32.3043	-4.4186	17.1319
4	4.3206	1.1641	0.2209	4.3712	1.2195	1.7997	0.019	1.116	-0.9566	-0.585	-0.0167	-0.6094	0.1994	0.302	-0.0537	0.6637	0.2162	0.123	0.7223	-0.0512	0.5661	21.8232	-15.8918	-19.0126
5	7.9	5.3023	-1.9828	6.7801	-1.3506	2.3535	0.681	0.8075	0.5041	0.4274	-0.1326	0.3485	-0.275	0.0629	-0.4641	0.5514	0.1522	0.1483	0.6072	0.0314	0.5337	18.8627	-9.8586	-13.6392
6	1.7215	0.4439	-0.4894	1.1546	0.4941	1.5812	-0.1984	0.7188	-0.2041	-0.6262	-0.0321	-0.7545	0.1749	0.7004	-0.5645	1.0412	0.386	0.502	1.1565	0.0643	0.6275	27.3271	-8.3977	-29.4282
7	1.7953	-1.1677	-1.0096	1.0292	-0.2204	3.1999	0.058	0.5753	-1.2005	-0.5368	-0.4049	-0.2375	0.8668	0.2597	0.052	1.0729	0.1909	0.151	0.7766	-0.2067	0.9394	19.4303	-26.5295	-22.7426
8	4.2538	0.7421	-0.001	4.5632	0.1918	2.3564	-0.0873	0.5506	-1.2951	-0.1483	0.1882	-1.433	0.5639	0.8365	-0.0181	0.7687	0.3099	0.1234	0.8314	0.012	0.7242	30.6155	-17.8218	-12.771
9	4.6251	2.536	-0.9698	5.6245	-0.7482	3.4826	0.0152	0.0223	-0.422	-0.1653	-0.1838	-1.0459	0.3092	0.6608	0.0257	0.4597	0.2214	0.1083	0.721	0.1019	0.7156	28.1037	-15.5453	-5.9285
10	4.6894	-0.4548	1.0407	1.2973	-1.1771	4.7519	-0.1491	-0.3973	-1.4077	-0.2587	-0.077	0.7267	1.0222	-0.6074	0.2185	0.6673	-0.1406	-0.0013	0.47	-0.2604	1.4265	-14.7472	-22.9986	-5.9491
11	3.0036	-2.9873	1.2667	2.8319	-1.5509	2.8372	0.1209	-0.2689	-0.4726	-0.3557	-0.3033	0.9487	0.6215	-0.7366	0.273	0.5853	-0.162	-0.0881	0.6514	-0.1991	1.2419	-16.423	-16.6285	-6.4065
12	4.2741	-1.3766	-1.8183	0.4721	0.8332	3.0581	-0.7466	-0.4448	-1.4123	-0.93	-0.2698	1.1811	0.8352	-0.7877	0.0391	1.1333	-0.3473	-0.0966	0.458	-0.0078	1.3699	-14.1846	-32.8057	-2.2711
13	2.9556	0.1991	0.1215	3.0077	0.5423	3.0513	0.151	0.6635	-1.207	-0.6311	-0.3908	1.1358	0.4668	-0.5264	0.2769	0.8768	0.0163	-0.1645	0.7134	-0.4272	1.2475	-10.175	-22.3461	-17.6087
14	1.9298	-0.6757	-1.8053	0.8382	0.9797	2.5655	-0.4796	-0.6857	-0.5284	0.6675	0.292	0.0446	0.6687	0.3021	0.1859	0.9324	0.2842	0.0258	0.903	0.2323	0.6182	14.8242	-20.1764	19.7801
15	1.9808	-1.6591	-1.7727	3.5627	3.4563	3.2288	-0.7247	-0.6679	-0.3173	0.3534	0.2428	0.4031	-0.2646	1.0539	0.4912	0.847	0.1891	-0.0029	0.7605	0.1905	0.5194	10.6304	-13.8798	15.619
16	3.5712	0.6053	-0.2227	2.3516	0.1391	1.001	-0.5123	-0.9677	-0.3318	1.3487	0.1288	-0.132	0.1948	0.7114	0.2321	1.3459	0.5821	-0.2135	1.3763	0.3436	0.4582	19.0644	-13.9719	31.7636
17	3.5459	1.6425	0.4804	0.9451	1.0485	4.5176	-0.2145	0.1501	-0.9548	1.329	0.6215	-0.1793	0.6539	0.0089	0.5085	1.233	0.4263	0.1368	0.8557	0.4912	0.8851	21.1861	-29.5019	17.0023
18	4.7831	-1.2442	-4.0934	2.8186	2.0757	6.1036	-1.1633	-0.7573	-0.9433	0.8368	0.6855	0.7755	1.2381	0.3912	0.5503	1.1879	0.2226	0.1992	0.8071	0.3772	0.931	5.7355	-24.9492	23.5575
19	2.7697	-0.8571	-1.0641	0.5467	1.1516	7.5438	-0.5033	-0.6783	-0.8539	1.126	0.3932	0.3113	0.7579	0.1144	0.2488	0.9539	0.2015	0.26	0.6697	0.3113	0.8526	0.5179	-22.0305	18.6931
20	4.2912	0.1544	0.2307	2.4219	0.0332	1.8662	0.4247	1.2938	-0.0605	-0.6259	-0.4138	-0.2084	0.1873	0.1176	-0.0163	0.9646	0.2869	0.1361	0.9051	-0.0359	0.478	13.1241	-5.9981	-29.8684
21	5.7249	4.4362	0.9759	9.5706	1.9876	0.8264	0.4584	1.1411	-0.0661	0.3898	0.084	-0.1788	0.094	0.2976	-0.4957	0.7432	0.1467	0.0645	0.7289	-0.0307	0.4077	9.0679	-4.2677	-22.3816
22	3.4019	-0.1957	-0.1184	1.4535	0.2289	0.8068	0.4014	1.4538	-0.198	-1.4253	-0.2265	-0.0325	0.0977	0.0573	-0.1115	1.1087	0.3513	0.1488	1.1714	-0.1327	0.5929	16.9449	-11.3497	-32.9855
23	2.9048	-0.4426	-0.9827	2.9298	-1.4016	1.8335	0.3405	1.3599	-0.2228	-1.2228	-0.3134	0.1271	-0.0929	-0.1663	-0.0576	1.1452	0.3373	-0.0561	1.1375	-0.0624	0.4184	2.194	-1.7446	-33.5997
24	1.8784	-1.2099	0.3638	2.4686	0.5348	3.5955	0.3204	0.7171	1.0059	-0.4694	-0.0947	-1.6395	-0.8359	0.952	-0.1997	0.6395	-0.2752	0.1542	0.771	0.1807	1.4409	29.3156	22.1106	-6.7296
25	6.2664	-3.764	4.8631	4.0526	-1.6846	5.917	0.422	-0.5779	1.1108	-0.6136	-0.1286	-1.1216	0.3582	-0.3314	-0.0024	0.5246	-0.1767	0.1189	0.7833	0.1344	0.9551	23.4955	16.0017	-4.6589
26	0.5977	0.0401	0.3486	0.4429	1.0305	2.4632	-0.2699	-0.1344	0.7072	0.0063	0.5287	-0.7394	-0.3855	1.6727	-0.0494	0.6711	-0.3432	-0.1703	0.9766	-0.1259	1.7398	36.2266	24.5223	5.2862
27	1.7896	0.8222	0.7403	1.7278	1.8704	2.0459	0.3509	-0.1044	0.061	-0.5227	-0.2354	-1.4915	-1.0457	0.8145	0.1237	1.0542	-0.1642	0.377	0.8877	0.2393	1.7119	30.0066	31.3253	-14.0073
28	3.2998	-0.7625	2.8813	4.114	-3.0323	6.9178	0.2702	1.0227	0.3289	-0.3861	-0.4721	-1.0384	-0.3133	1.1807	-0.0598	0.6957	-0.1416	0.3853	1.0415	0.2577	1.5543	36.0511	15.1526	-11.4809
29	2.3048	-0.4583	1.8268	3.6857	-0.6561	7.1528	0.0697	0.0741	0.3849	-0.5149	0.04	-1.0774	0.0735	0.4278	-0.1066	0.4906	-0.0523	0.2115	0.9084	0.1505	0.944	31.4994	8.0742	-9.6621
30	2.6337	-3.1731	2.9235	3.8238	-3.5248	3.2381	0.384	0.4388	0.826	-0.3675	-0.2917	-0.4216	-0.345	0.5665	0.3596	0.6774	-0.497	1.1266	1.3248	1.0339	0.9699	31.9569	13.0281	-25.3982

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 157 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 39 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 40 through 68 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 69 through 82 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 83 through 95 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 124 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 125 through 157 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 9 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 82 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 83 through 95 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 96 through 157 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 39 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 40 through 67 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 68 through 82 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 83 through 95 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 96 through 124 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 125 through 157 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 8 through 39 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 40 through 67 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 68 through 95 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 96 through 157 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 8 through 39 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 40 through 67 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 68 through 82 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 83 through 95 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 96 through 124 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 125 through 150 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 151 through 157 )

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