PDB-6gq8: Superoxide reductase from Nanoarchaeum equitans

ID or keywords:

Entry

Database: PDB / ID: 6gq8

Title

Superoxide reductase from Nanoarchaeum equitans

Components

NEQ011

Keywords

OXIDOREDUCTASE / neelaredoxin / superoxide anion / reactive oxygen species / archaea / enzyme

Function / homology

Function and homology information

oxidoreductase activity / iron ion binding
Similarity search - Function

Biological species

Nanoarchaeum equitans Kin4-M (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Romao, C.V. / Matias, P.M. / Teixeira, M. / Bandeiras, T.M.

Funding support

Portugal, 5items

Organization	Grant number	Country
	Fundacao para a Ciencia e Tecnologia - PTDC/BIA-PRO/111940/2009	Portugal
	Fundacao para a Ciencia e Tecnologia - PTDC/BBB-BQB/3135/2014	Portugal
	Fundacao para a Ciencia e Tecnologia-MOSTMICRO -LISBOA-01-0145-FEDER-007660	Portugal
	Fundacao para a Ciencia e Tecnologia - iNOVA4Health - LISBOA-01-0145-FEDER-007344	Portugal
	Fundacao para a Ciencia e Tecnologia - SFRH/BPD/94050/2013	Portugal

Citation

Journal: Biochemistry / Year: 2018
Title: Insights into the Structures of Superoxide Reductases from the Symbionts Ignicoccus hospitalis and Nanoarchaeum equitans.
Authors: Romao, C.V. / Matias, P.M. / Sousa, C.M. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Bandeiras, T.M.

History

Deposition	Jun 7, 2018	Deposition site: PDBE / Processing site: PDBE
Supersession	Jun 20, 2018	ID: 4BV1
Revision 1.0	Jun 20, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2018	Group: Data collection / Database references / Category: citation 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
Revision 1.2	Sep 19, 2018	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.title / _citation_author.identifier_ORCID
Revision 1.3	Jan 17, 2024	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

-
Download

PDBx/mmCIF format	6gq8.cif.gz	197.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6gq8.ent.gz	159.3 KB	Display	PDB format
PDBx/mmJSON format	6gq8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6gq8_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	6gq8_full_validation.pdf.gz	2.2 MB	Display
Data in XML	6gq8_validation.xml.gz	18.3 KB	Display
Data in CIF	6gq8_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gq/6gq8 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gq8	HTTPS FTP

-
Related structure data

Related structure data	1dqiS S: Starting model for refinement
Similar structure data	4bv1-d 1uuq-d 5yae-d 4lbh-1 4lbi-d 6trh-3 4px1-d 1odz-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NEQ011

B: NEQ011

C: NEQ011

D: NEQ011

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, The biological Unit is a tetramer

Unit cell

Length a, b, c (Å)	51.880, 82.010, 91.300
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NEQ011 Mass: 12737.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Gene: NEQ011 / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q74MF3
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 36 % Description: Blue Crystals with shape of a truncated rectangular pyramid
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 25% (w/v) PEG 2000 MME

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2010 / Details: Bent Cylindrical Mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.88→45.1 Å / Num. obs: 31984 / % possible obs: 98.6 % / Redundancy: 4.1 % / B_iso Wilson estimate: 28 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.03 / R_rim(I) all: 0.062 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.88→1.95 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.383 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2864 / CC_1/2: 0.858 / R_pim(I) all: 0.237 / R_rim(I) all: 0.453 / % possible all: 91.6

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DQI

1dqi

Resolution: 1.9→45.1 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.62

	R_factor	Num. reflection	% reflection
R_free	0.2404	1580	5.09 %
R_work	0.2059	-	-
obs	0.2077	31054	98.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→45.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3600	0	4	115	3719

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3709
X-RAY DIFFRACTION	f_angle_d	0.501	5017
X-RAY DIFFRACTION	f_dihedral_angle_d	13.93	2233
X-RAY DIFFRACTION	f_chiral_restr	0.051	526
X-RAY DIFFRACTION	f_plane_restr	0.004	633

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 (%)
1.9001-1.9614	0.349	125	0.3213	2503	X-RAY DIFFRACTION	94
1.9614-2.0315	0.3196	147	0.2882	2635	X-RAY DIFFRACTION	99
2.0315-2.1128	0.3039	127	0.263	2685	X-RAY DIFFRACTION	100
2.1128-2.209	0.2882	148	0.2584	2654	X-RAY DIFFRACTION	100
2.209-2.3255	0.278	142	0.2362	2689	X-RAY DIFFRACTION	100
2.3255-2.4712	0.2558	128	0.2386	2705	X-RAY DIFFRACTION	100
2.4712-2.6619	0.3059	157	0.2387	2644	X-RAY DIFFRACTION	100
2.6619-2.9298	0.2837	162	0.2379	2706	X-RAY DIFFRACTION	100
2.9298-3.3536	0.2253	145	0.2071	2704	X-RAY DIFFRACTION	100
3.3536-4.2247	0.2252	141	0.1737	2753	X-RAY DIFFRACTION	100
4.2247-45.119	0.184	158	0.1592	2796	X-RAY DIFFRACTION	97

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	7.8193	-1.9692	-1.2467	4.9656	0.572	3.7091	0.6134	0.2963	-0.8904	-0.6213	-0.3955	0.7706	0.1586	-0.4007	-0.2148	0.4694	0.0387	-0.2318	0.3381	-0.0441	0.6767	-21.6637	-18.5003	13.185
2	4.5231	-0.8354	-1.1982	2.9104	-0.9087	1.6557	0.2022	0.5274	-1.4543	-0.6949	-0.1035	-0.056	0.485	-0.0123	-0.2377	0.5292	0.0201	-0.1567	0.3318	-0.0575	0.847	-10.1301	-23.5888	18.8318
3	6.9513	-2.6809	3.4458	6.2327	-1.3604	6.9439	0.1557	0.9422	0.3735	-0.9291	-0.1832	0.7565	0.1335	-0.3555	-0.0858	0.3317	0.0041	-0.0898	0.388	0.0814	0.4502	-22.6518	-7.694	12.8637
4	6.2844	-1.2317	1.8288	3.8224	-0.8176	2.5407	0.0921	0.0614	-0.7518	0.2209	0.0345	0.6578	0.0101	0.0228	-0.1841	0.2876	-0.0015	-0.014	0.2319	-0.0038	0.4696	-18.1082	-15.1502	23.111
5	9.1225	0.545	1.8607	3.1448	-0.1352	3.3087	0.1756	1.4603	-0.3415	-0.3926	-0.3733	0.3376	0.0607	0.0557	0.2121	0.407	0.0904	-0.1185	0.4774	-0.1587	0.4061	-15.7017	-14.6551	11.2795
6	7.2565	-1.1351	-0.6678	3.9261	-0.3144	4.446	0.339	0.4361	1.0505	-0.8745	-0.1752	-0.7665	-0.3423	-0.2895	-0.2749	0.3647	-0.0266	0.2097	0.389	0.1381	0.569	-3.5623	4.9133	14.2623
7	5.51	-1.9809	-0.5872	3.0016	0.7192	3.4379	0.1653	1.5527	1.3295	-0.1971	-0.1326	0.1454	-0.6167	-0.5397	-0.1672	0.4887	0.0413	0.0783	0.5359	0.1495	0.5691	-15.4688	9.8138	19.356
8	1.8891	-1.3631	-2.6663	5.953	0.8006	7.4729	0.0954	0.5813	-0.749	-1.1437	-0.0066	-0.6844	0.2327	0.6069	-0.0403	0.329	0.0147	0.0694	0.4115	-0.0496	0.4151	-2.599	-5.8227	13.4624
9	4.5485	-0.2496	-0.9391	4.5497	0.1322	3.2032	0.1743	0.4334	0.0715	0.0722	-0.1848	-0.1606	-0.0809	-0.1464	-0.0724	0.1854	-0.0028	0.01	0.1718	0.049	0.1736	-7.7653	1.2352	23.6788
10	4.6153	-0.3431	0.4267	2.7092	1.3258	3.5831	1.2278	1.7594	0.3304	-0.851	-0.7068	-0.1365	-0.6319	0.0153	-0.2037	0.4125	0.1485	0.0469	0.4975	0.1278	0.2922	-9.4519	1.2333	11.8275
11	5.9591	-2.7704	0.5362	5.4647	-1.5364	4.6861	0.0345	-0.5053	0.1594	0.4306	-0.0672	-0.6314	0.1307	0.1041	0.0559	0.4144	-0.0697	-0.0797	0.3491	-0.0871	0.4837	-3.0117	3.3987	38.9271
12	3.3844	-0.032	-0.1601	0.8138	0.0771	2.7379	0.1832	-0.2168	-0.4158	0.9505	-0.0991	-1.7147	0.6384	0.4712	-0.1874	0.4821	0.0293	-0.191	0.4669	0.0245	0.7782	3.6735	-7.6355	33.6285
13	6.5561	-1.3461	0.5655	4.6062	1.1673	2.8241	0.069	-1.0147	0.2818	0.8602	0.0501	0.471	0.1912	-0.1945	-0.1716	0.4092	-0.0396	0.0808	0.3436	0.0274	0.2366	-13.5458	2.7742	38.7443
14	4.0599	-0.3214	-0.0599	4.9755	2.0162	2.3298	-0.051	-0.2469	0.051	0.6618	0.1306	-0.351	0.1316	0.1075	-0.102	0.2519	0.0098	-0.0151	0.1781	0.084	0.1724	-5.6505	-0.8248	28.9464
15	3.5896	-0.78	-0.7845	2.268	1.1424	2.723	-0.1655	-0.4372	0.1516	1.2709	0.3064	-0.2176	0.3524	0.3864	-0.0353	0.4376	-0.0122	-0.0904	0.4269	0.0059	0.3437	-6.0745	-3.0079	40.82
16	4.0374	-2.044	-1.1999	6.4286	0.4016	4.0252	0.3023	-0.2106	-0.5442	0.4054	-0.4405	1.175	-0.1384	-0.3206	0.0859	0.4591	-0.117	0.1293	0.4521	0.2146	0.8889	-23.8988	-17.6338	37.9626
17	1.7181	-0.6886	1.4378	3.8651	1.6441	2.7117	0.1824	-0.3613	-0.1127	0.4678	-0.0587	1.6112	-0.2013	-0.8073	-0.219	0.5096	-0.0642	0.1533	0.4465	0.0939	0.8776	-30.2425	-6.5716	32.3782
18	1.8314	-1.6513	-0.2527	7.0622	-2.2695	5.4963	-0.0067	-0.9827	-0.76	1.4093	0.0659	-0.8631	0.1374	0.3168	-0.0919	0.4315	-0.0701	-0.1472	0.3557	0.1377	0.6044	-13.0908	-17.2882	38.6691
19	3.854	-0.7579	0.53	4.7824	-1.9449	2.3574	0.1727	0.0327	-0.5387	0.17	-0.1276	0.2751	0.1587	-0.1061	-0.1395	0.2637	-0.0111	-0.0328	0.2276	0.0238	0.3895	-20.5931	-13.238	28.2929
20	2.3181	0.5573	-0.2997	9.1419	-0.5742	1.9972	0.1047	-0.761	-0.1628	1.1027	-0.1412	0.1833	-0.164	-0.2957	0.0209	0.4187	-0.0621	0.0848	0.4208	0.1699	0.3901	-21.0418	-11.2915	40.1792

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:25)
2	X-RAY DIFFRACTION	2	(chain A and resid 26:44)
3	X-RAY DIFFRACTION	3	(chain A and resid 45:55)
4	X-RAY DIFFRACTION	4	(chain A and resid 56:88)
5	X-RAY DIFFRACTION	5	(chain A and resid 89:109)
6	X-RAY DIFFRACTION	6	(chain B and resid 1:25)
7	X-RAY DIFFRACTION	7	(chain B and resid 26:44)
8	X-RAY DIFFRACTION	8	(chain B and resid 45:55)
9	X-RAY DIFFRACTION	9	(chain B and resid 56:88)
10	X-RAY DIFFRACTION	10	(chain B and resid 89:109)
11	X-RAY DIFFRACTION	11	(chain C and resid 1:25)
12	X-RAY DIFFRACTION	12	(chain C and resid 26:44)
13	X-RAY DIFFRACTION	13	(chain C and resid 45:55)
14	X-RAY DIFFRACTION	14	(chain C and resid 56:88)
15	X-RAY DIFFRACTION	15	(chain C and resid 89:109)
16	X-RAY DIFFRACTION	16	(chain D and resid 1:25)
17	X-RAY DIFFRACTION	17	(chain D and resid 26:44)
18	X-RAY DIFFRACTION	18	(chain D and resid 45:55)
19	X-RAY DIFFRACTION	19	(chain D and resid 56:88)
20	X-RAY DIFFRACTION	20	(chain D and resid 89:109)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi