PDB-4bfk: Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E...

ID or keywords:

Entry

Database: PDB / ID: 4bfk

Title

Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E12Q mutant

Components

SUPEROXIDE REDUCTASE

Keywords

OXIDOREDUCTASE / OXYGEN DETOXIFICATION

Function / homology

Function and homology information

superoxide reductase / superoxide reductase activity / iron ion binding
Similarity search - Function

Biological species

ARCHAEOGLOBUS FULGIDUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.103 Å

Authors

Bandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V.

Citation

Journal: To be Published
Title: Understanding the Role of Key Residues in the Superoxide Reductase Molecular Mechanism, Exploring Archaeoglobus Fulgidus Sor Structure
Authors: Bandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V.

History

Deposition	Mar 19, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bfk.cif.gz	211.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4bfk.ent.gz	171.8 KB	Display	PDB format
PDBx/mmJSON format	4bfk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4bfk_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	4bfk_full_validation.pdf.gz	444.8 KB	Display
Data in XML	4bfk_validation.xml.gz	21.7 KB	Display
Data in CIF	4bfk_validation.cif.gz	30.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfk ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfk	HTTPS FTP

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Related structure data

Related structure data	4bffC 4bfjC 4c4bC 4c4uC 4bglS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4bff-4 4bff-2 4c4u-1 4bff-1 4c4u-2 4c4u-4 4c4u-3 4bgl-d 4bff-3 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

A: SUPEROXIDE REDUCTASE

B: SUPEROXIDE REDUCTASE

C: SUPEROXIDE REDUCTASE

D: SUPEROXIDE REDUCTASE

hetero molecules

55.1 kDa, 4 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)	93.316, 106.660, 99.162
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	SUPEROXIDE REDUCTASE / SOR Mass: 13711.564 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PT7-7/NAFE12QA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: O29903, superoxide reductase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.2 Å³/Da / Density % sol: 44 % / Description: NONE
Crystal grow	pH: 4.6 / Details: 0.1 M SODIUM ACETATE, PH 4.6 AND 12% PEG 300

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97925
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97925 Å / Relative weight: 1
Reflection	Resolution: 2.1→47 Å / Num. obs: 54088 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 12.86
Reflection shell	Resolution: 2.1→2.2 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 3.58 / % possible all: 96

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
XDS	PROGRAM PACKAGE	data reduction
XDS	PROGRAM PACKAGE	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGL

4bgl

Resolution: 2.103→46.968 Å / SU ML: 0.19 / σ(F): 1.02 / Phase error: 18.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2024	1458	5.1 %
R_work	0.1501	-	-
obs	0.1527	28616	98.32 %

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.103→46.968 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3867	0	4	248	4119

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4001
X-RAY DIFFRACTION	f_angle_d	1.01	5414
X-RAY DIFFRACTION	f_dihedral_angle_d	13.796	1396
X-RAY DIFFRACTION	f_chiral_restr	0.07	591
X-RAY DIFFRACTION	f_plane_restr	0.004	695

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 (%)
2.1032-2.1783	0.2687	134	0.1881	2599	X-RAY DIFFRACTION	95
2.1783-2.2655	0.2326	148	0.1688	2717	X-RAY DIFFRACTION	100
2.2655-2.3686	0.2185	146	0.1561	2742	X-RAY DIFFRACTION	100
2.3686-2.4935	0.2036	141	0.1518	2713	X-RAY DIFFRACTION	100
2.4935-2.6497	0.2512	158	0.1579	2727	X-RAY DIFFRACTION	100
2.6497-2.8543	0.2038	137	0.1534	2748	X-RAY DIFFRACTION	100
2.8543-3.1415	0.1943	168	0.1555	2704	X-RAY DIFFRACTION	99
3.1415-3.5959	0.193	135	0.1402	2749	X-RAY DIFFRACTION	98
3.5959-4.5299	0.1767	133	0.1348	2722	X-RAY DIFFRACTION	97
4.5299-46.98	0.1901	158	0.149	2737	X-RAY DIFFRACTION	95

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	6.5483	-1.8674	0.3921	1.3463	-2.2555	5.6138	-0.052	-0.2064	-0.32	0.1169	0.0708	-0.3775	0.8713	0.7227	-0.0371	0.3245	0.0914	-0.034	0.4122	0.0298	0.3122	44.2247	11.2577	-13.1555
2	4.5385	-0.1812	1.4177	3.5126	-3.7033	4.5345	0.2879	0.5852	0.2393	-0.3713	0.0121	-0.0399	0.7784	-0.1352	-0.3124	0.2799	0.0862	0.0902	0.342	-0.0206	0.2362	36.3639	12.9997	-32.4747
3	3.2032	-0.872	2.0013	4.7331	-3.5007	3.3138	0.2364	0.6229	-0.3038	-0.4607	0.2085	0.269	0.3422	0.3406	-0.3474	0.2983	0.0788	0.0609	0.3059	-0.0419	0.187	32.8657	15.7164	-33.8298
4	1.6511	0.3703	-0.0432	3.3299	-1.7374	3.5619	-0.2377	0.0678	-0.3413	0.0524	0.1816	-0.3083	0.576	-0.0747	-0.0013	0.206	0.065	0.0432	0.1714	-0.0119	0.2158	34.2697	10.6873	-16.9798
5	5.9876	-2.1846	-2.1572	2.9582	-2.222	5	-0.1031	0.8423	0.3739	-1.0794	0.2489	-0.9796	-0.6328	0.8731	-0.1413	0.3212	-0.1741	0.1057	0.3921	0.0033	0.3226	39.1556	33.6204	-27.5175
6	3.7067	2.3001	-0.2292	2.449	-2.0578	3.6638	-0.0033	0.0763	0.2657	0.0163	0.265	0.5339	0.0682	0.2005	-0.2828	0.146	0.0092	0.0214	0.1187	-0.0002	0.1619	29.0466	21.8601	-21.5295
7	2.2586	1.3407	-1.5467	2.7209	-2.3737	4.1683	-0.1416	-0.0281	-0.1081	-0.4167	0.044	-0.0244	0.7107	0.1722	0.0524	0.2274	0.0116	-0.0049	0.0882	-0.0244	0.159	26.3805	8.9866	-18.9708
8	0.6067	1.8863	-1.6765	5.7908	-5.3734	4.9464	-0.0217	-0.1078	-0.0169	0.0582	-0.1429	-0.2146	0.0811	0.5338	0.2106	0.1267	0.005	0.0126	0.1901	0.0218	0.1999	37.7392	18.5292	-19.1944
9	1.4697	0.1303	0.8378	1.8696	-0.3539	5.4916	0.1564	0.1897	0.1333	-0.2074	-0.1968	-0.2589	0.1856	1.0815	0.1271	0.1525	0.1279	0.0311	0.2464	-0.0092	0.2483	40.2772	17.0396	-21.4449
10	4.381	1.6024	0.9836	5.5382	-2.1755	5.173	0.083	-1.0543	0.8104	1.1615	-0.0705	-0.4951	-0.6327	1.1656	-0.1694	0.4064	-0.142	-0.097	0.5006	-0.1091	0.4567	40.028	35.1903	-11.9927
11	3.0927	-0.6755	1.9718	2.7219	1.0841	2.1247	0.1052	-0.0854	0.3179	0.1736	-0.2856	-0.0092	-1.4478	0.6974	-0.0933	0.3453	-0.057	-0.0011	0.1459	-0.0592	0.1784	30.5749	35.365	-2.168
12	1.0676	0.6524	-0.6549	2.2644	1.4882	2.3417	0.3205	-0.1379	0.2422	0.2312	0.2023	0.5226	-0.41	-0.1832	-0.4772	0.0758	0.0045	0.0329	0.1375	0.0098	0.1434	26.1672	28.0325	3.0524
13	1.2546	-0.2535	0.7478	0.5855	-1.0086	2.6142	-0.3127	-0.1445	0.336	0.4252	0.1795	-0.1514	-0.7971	-0.1471	0.078	0.2395	0.014	-0.04	0.1173	-0.0305	0.1986	28.0317	33.7546	-11.8027
14	5.3113	-0.3222	-4.2737	2.6025	1.2041	3.7886	-0.0116	-1.7103	-0.2099	1.0194	0.7271	-0.7456	0.6076	1.4383	-0.792	0.2887	0.0709	-0.1019	0.4009	-0.0141	0.3119	41.6752	15.564	0.2889
15	1.7382	-0.9234	1.3027	1.3163	-1.0119	3.3326	0.0093	-0.0213	-0.044	0.1866	0.0149	0.2812	-0.3623	-0.2872	-0.0516	0.1027	0.0464	-0.007	0.1345	-0.0014	0.194	18.6958	31.9006	-16.2808
16	3.6562	0.2274	0.3046	4.4358	-0.9462	3.2382	0.4368	-0.1793	-0.3546	0.0598	-0.3466	0.1067	0.3261	0.4148	-0.132	0.2007	-0.02	0.0175	0.2401	-0.0268	0.1042	28.4529	22.9624	3.1146
17	2.0395	-1.0717	3.5559	1.1344	-1.7964	6.4307	0.0506	-0.0753	0.294	0.1642	-0.04	0.0678	-0.3735	0.6718	0.1679	0.1367	-0.0356	-0.0193	0.2698	-0.0221	0.1327	34.4106	28.3617	-8.9338
18	3.0644	0.152	-1.0418	0.5435	0.3978	4.1005	-0.0098	-0.1749	0.0907	0.1581	-0.2054	-0.0537	-0.0857	1.0144	0.1303	0.1372	-0.0643	-0.019	0.068	-0.0218	0.2142	35.5024	30.7809	-6.3559
19	4.008	-1.6852	-0.4267	5.4561	1.4902	2.7974	0.0545	0.4815	-0.1742	-0.4189	-0.1494	0.2909	0.7003	-0.7138	0.3195	0.3005	-0.113	-0.0189	0.4116	0.0247	0.3024	6.0071	17.5504	-28.9199
20	2.8736	-2.1346	0.6826	9.0759	-1.9972	2.3427	-0.1902	0.3849	-0.1966	-0.3641	0.1809	-0.1919	0.3832	0.1141	0.0082	0.3246	-0.0546	0.0587	0.1701	-0.0724	0.1724	20.2455	4.5386	-28.7852
21	1.4256	0.7478	-0.4765	3.4106	-1.7004	2.1177	-0.0632	0.0779	-0.1033	-0.2528	-0.0017	0.1484	0.42	-0.3348	0.0156	0.1807	-0.0779	0.01	0.1952	-0.0159	0.1552	16.1291	15.0352	-23.167
22	0.8277	-0.1448	0.4146	2.2938	0.6945	1.2612	-0.0065	0.0653	0.0212	-0.1483	-0.0739	0.1073	0.0512	0.005	0.1105	0.0664	-0.0216	0.0269	0.1388	0.0034	0.1104	24.7751	20.0436	-27.0979
23	1.3238	-0.9344	-0.314	8.1327	-0.8248	1.3337	0.1118	0.0155	-0.1231	-0.4068	-0.2362	0.4243	0.2204	-0.2642	0.0792	0.109	-0.0769	0.0019	0.2165	0.0032	0.1484	11.6775	12.3967	-24.2099
24	4.32	-1.3017	-2.4469	5.9074	1.034	4.3289	0.1207	-0.4082	0.4456	0.4712	-0.3357	0.44	-0.0896	-1.0138	0.14	0.2992	-0.1381	0.0855	0.5616	-0.0077	0.384	5.0859	13.1707	-4.0802
25	1.6908	-1.4078	0.0065	2.5906	0.1711	1.1513	-0.1767	-0.3296	0.0933	0.3182	0.2013	0.2052	-0.0375	-0.4333	-0.013	0.2025	0.0337	0.0609	0.2428	-0.0285	0.1886	13.3398	23.159	-3.0871
26	3.9942	-0.4278	2.8995	2.8449	-1.6626	4.7803	-0.1689	0.0304	0.4624	0.0545	-0.1046	0.2431	-0.2311	-0.5553	0.1932	0.1225	0.0837	-0	0.2572	-0.0268	0.1735	10.336	28.0171	-17.0435
27	2.4028	-1.227	0.0661	2.0903	0.308	2.4083	-0.0265	-0.2969	-0.031	0.2082	0.0436	0.0932	0.0759	-0.2003	-0.026	0.1166	-0.0379	0.0068	0.1465	-0.0073	0.1191	22.8088	20.5697	-2.8762
28	1.7033	-2.3591	0.0943	6.2837	-0.1353	2.0688	-0.1142	-0.1748	-0.025	0.4445	0.1223	0.5781	0.0691	-0.6309	0.0246	0.1593	-0.0251	0.0614	0.2939	-0.0033	0.2185	8.034	20.8852	-7.9857

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 2:16)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 17:23)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 24:33)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 34:57)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 58:63)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 64:70)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 71:101)
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESSEQ 102:110)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 111:125)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 1:10)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 11:24)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 25:33)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 34:57)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 58:63)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 64:90)
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESSEQ 91:101)
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESSEQ 102:110)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 111:125)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 1:15)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 16:34)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ 35:70)
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESSEQ 71:101)
23	X-RAY DIFFRACTION	23	CHAIN C AND (RESSEQ 102:125)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 1:15)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 16:57)
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESSEQ 58:70)
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESSEQ 71:101)
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESSEQ 102:125)

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Yorodumi