PDB-5mab: FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2...

ID or keywords:

Entry

Database: PDB / ID: 5mab

Title

FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase

Components

FoxE

Keywords

ELECTRON TRANSPORT / cytochrome-c / electron transfer / photoferrotrophy

Function / homology

metal ion binding / COPPER (II) ION / HEME C / PHOSPHATE ION / FoxE

Function and homology information

Biological species

Rhodobacter sp. SW2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.436 Å

Authors

Pereira, L. / Saraiva, I.H. / Oliveira, A.S. / Soares, C. / Gomes, R.O. / Frazao, C.

Funding support

Portugal, 2items

Citation

Journal: To be published
Title: FoxE P3121 crystal structure of Rhodopseudomonas ferrooxidans SW2 putative iron oxidase
Authors: Pereira, L. / Saraiva, I.H. / Coelho, R.

History

Deposition	Nov 3, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/5mab ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5mab	HTTPS FTP

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Related structure data

Related structure data	5mvoC C: citing same article (ref.)
Similar structure data	5mvo-d 1wta-1 3wcd-2 6zz5-d 3wcf-2 3wcj-2 3wsa-2 3wcf-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
Related items in Molecule of the Month	#36 - Dec 2002 Cytochrome c similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: FoxE

B: FoxE

C: FoxE

hetero molecules

99.2 kDa, 3 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)	112.770, 112.770, 143.540
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-446- HOH

#1: Protein	FoxE Mass: 31599.607 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sp. SW2 (bacteria) / Gene: foxE / Plasmid: pUX19 / Production host: Escherichia coli (E. coli) / Variant (production host): JCB7123 / References: UniProt: A3DTD8
#2: Chemical	ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Formula: C₃₄H₃₄FeN₄O₄
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 54 % / Description: Polyhedron
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: VAPOR DIFFUSION AT 293 K IN SITTING DROPS OF 1 MICRO-L OF PROTEIN SOLUTION (15 MG/ML OF FOXE IN 5 MM POTASSIUM PHOSPHATE BUFFER PH 7.0) PLUS 1 MICRO-L OF PRECIPITANT SOLUTION (1.2 M ...Details: VAPOR DIFFUSION AT 293 K IN SITTING DROPS OF 1 MICRO-L OF PROTEIN SOLUTION (15 MG/ML OF FOXE IN 5 MM POTASSIUM PHOSPHATE BUFFER PH 7.0) PLUS 1 MICRO-L OF PRECIPITANT SOLUTION (1.2 M SODIUM/POTASSIUM PHOSPHATE PH 7.5, 50 MM COPPER CHLORIDE) EQUILIBRATED AGAINST 500 ML OF PRECIPITANT SOLUTION IN THE WELL

Crystal

Density Matthews: 2.67 Å³/Da / Density % sol: 54 % / Description: Polyhedron

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOR DIFFUSION AT 293 K IN SITTING DROPS OF 1 MICRO-L OF PROTEIN SOLUTION (15 MG/ML OF FOXE IN 5 MM POTASSIUM PHOSPHATE BUFFER PH 7.0) PLUS 1 MICRO-L OF PRECIPITANT SOLUTION (1.2 M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.739 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.739 Å / Relative weight: 1
Reflection	Resolution: 2.43→97.7 Å / Num. obs: 38579 / % possible obs: 96.1 % / Redundancy: 32.3 % / B_iso Wilson estimate: 56 Å² / R_merge(I) obs: 0.136 / Net I/σ(I): 28.3
Reflection shell	Resolution: 2.43→2.54 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.707 / Mean I/σ(I) obs: 1.9 / CC_1/2: 0.482 / % possible all: 77.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.436→97.662 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.29 / Stereochemistry target values: LS_WUNIT_K1

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1686	38575	100 %	thin shells
R_work	0.1686	-	-	-
obs	0.1686	38575	96.36 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.436→97.662 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5931	0	294	101	6326

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	6465
X-RAY DIFFRACTION	f_angle_d	1.287	8864
X-RAY DIFFRACTION	f_dihedral_angle_d	13.298	2304
X-RAY DIFFRACTION	f_chiral_restr	0.049	922
X-RAY DIFFRACTION	f_plane_restr	0.008	1163

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 (%)
2.4358-2.4635	0.5339	901	0.5339	901	X-RAY DIFFRACTION	68
2.4635-2.4924	0.4237	1012	0.4237	1012	X-RAY DIFFRACTION	78
2.4924-2.5228	0.4129	1086	0.4129	1086	X-RAY DIFFRACTION	82
2.5228-2.5548	0.3945	1110	0.3945	1110	X-RAY DIFFRACTION	84
2.5548-2.5884	0.3661	1161	0.3661	1161	X-RAY DIFFRACTION	89
2.5884-2.6239	0.3352	1199	0.3352	1199	X-RAY DIFFRACTION	91
2.6239-2.6614	0.3381	1275	0.3381	1275	X-RAY DIFFRACTION	98
2.6614-2.7011	0.3628	1326	0.3628	1326	X-RAY DIFFRACTION	100
2.7011-2.7433	0.3407	1317	0.3407	1317	X-RAY DIFFRACTION	100
2.7433-2.7883	0.2852	1319	0.2852	1319	X-RAY DIFFRACTION	100
2.7883-2.8364	0.2707	1321	0.2707	1321	X-RAY DIFFRACTION	100
2.8364-2.8879	0.2564	1327	0.2564	1327	X-RAY DIFFRACTION	100
2.8879-2.9435	0.2402	1323	0.2402	1323	X-RAY DIFFRACTION	100
2.9435-3.0036	0.2305	1315	0.2305	1315	X-RAY DIFFRACTION	100
3.0036-3.0689	0.2268	1337	0.2268	1337	X-RAY DIFFRACTION	100
3.0689-3.1403	0.2071	1324	0.2071	1324	X-RAY DIFFRACTION	100
3.1403-3.2188	0.2011	1335	0.2011	1335	X-RAY DIFFRACTION	100
3.2188-3.3058	0.1937	1334	0.1937	1334	X-RAY DIFFRACTION	100
3.3058-3.4031	0.1944	1309	0.1944	1309	X-RAY DIFFRACTION	100
3.4031-3.513	0.1662	1350	0.1662	1350	X-RAY DIFFRACTION	100
3.513-3.6385	0.1528	1331	0.1528	1331	X-RAY DIFFRACTION	100
3.6385-3.7842	0.1378	1325	0.1378	1325	X-RAY DIFFRACTION	100
3.7842-3.9565	0.1307	1323	0.1307	1323	X-RAY DIFFRACTION	100
3.9565-4.165	0.1098	1347	0.1098	1347	X-RAY DIFFRACTION	100
4.165-4.426	0.0992	1346	0.0992	1346	X-RAY DIFFRACTION	100
4.426-4.7677	0.1006	1357	0.1006	1357	X-RAY DIFFRACTION	100
4.7677-5.2475	0.1033	1357	0.1033	1357	X-RAY DIFFRACTION	100
5.2475-6.0067	0.1089	1357	0.1089	1357	X-RAY DIFFRACTION	100
6.0067-7.5674	0.1033	1404	0.1033	1404	X-RAY DIFFRACTION	100
7.5674-97.7402	0.1109	1447	0.1109	1447	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	0.1555	0.0024	-0.0519	0.4108	0.307	0.2455	-0.1069	0.6258	-0.1236	0.0943	0.0894	0.1522	-0.0537	0.3331	-0.0046	0.5812	-0.1141	0.0311	0.6211	0.0669	0.4404	39.6946	88.8948	17.1629
2	1.2043	-0.4521	-0.5713	0.3602	-0.265	1.4048	-0.0431	-0.0268	0.0872	-0.0296	0.0685	0.0583	0.1196	-0.2254	0	0.2183	-0.0622	-0.0345	0.2332	-0.0264	0.2437	43.7732	85.3247	45.3288
3	0.6632	-0.4907	0.4512	0.5549	-0.4754	0.4032	-0.0117	0.0855	0.0284	-0.0425	0.0143	0.0444	0.0957	0.027	-0	0.302	-0.0185	0.0057	0.2708	-0.0079	0.2599	54.9732	77.0735	45.9653
4	1.9982	-0.9794	-0.2052	1.7926	0.8218	0.5004	0.2761	0.2019	0.0686	-0.2293	0.0535	-0.0922	-0.0104	0.0887	-0.0003	0.4036	0.0383	0.0085	0.316	-0.0166	0.3086	67.3422	64.5944	39.5993
5	0.2497	0.433	0.3542	0.928	0.3129	1.1343	0.0246	0.0782	-0.0596	-0.2046	-0.0125	0.1201	0.2388	-0.0178	0	0.3032	-0.026	0.007	0.2534	-0.0174	0.2557	49.7971	78.6277	40.6983
6	0.1068	0.0628	-0.1418	0.2368	-0.0246	0.2056	-0.5913	0.4732	-0.8828	0.3102	-0.215	-0.4259	0.0451	0.175	-0.0433	0.3362	0.0157	-0.0164	0.3114	-0.0114	0.3637	49.4186	77.5872	51.6875
7	0.5159	0.1772	-0.2771	0.0677	-0.1193	0.2358	0.3003	0.4981	-0.2031	-0.2297	0.1303	0.3491	0.0728	-0.1143	0.0109	0.5382	0.0507	-0.0842	0.3056	-0.1084	0.3964	57.9029	65.011	38.1275
8	0.8549	0.78	-0.2915	0.7784	-0.0166	0.868	0.349	-0.5869	-0.3187	0.7546	-0.5151	0.0623	0.5318	-0.2584	-0.0072	0.4806	0.0087	0.0099	0.4099	0.0232	0.2515	50.6477	71.0537	63.0644
9	1.3908	0.557	-0.7239	0.3541	-0.5798	1.0398	0.2537	0.0071	0.2073	0.1303	-0.1494	0.1058	-0.1795	0.0744	0.0002	0.3248	-0.0229	0.0304	0.3103	-0.0359	0.3661	24.2995	80.7663	56.1422
10	0.6644	0.4152	-0.2809	0.2929	-0.2354	0.2294	0.2222	-0.1951	-0.1731	0.128	-0.045	0.1707	-0.0277	-0.0897	0.0007	0.2514	-0.0216	0.0065	0.3172	-0.0312	0.3343	15.9561	70.3409	59.9951
11	2.2807	2.1798	0.7557	2.8003	0.2794	0.5481	0.272	-0.11	-0.172	0.628	-0.3512	0.0169	0.2203	-0.175	-0.0068	0.3616	-0.0737	0.0246	0.3038	-0.0353	0.2894	8.5773	52.6475	63.3956
12	1.8026	1.3732	0.89	1.3577	0.2941	0.7782	0.1977	-0.0622	-0.0216	0.2701	-0.1245	0.0023	-0.0388	0.1071	0.0787	0.3932	-0.0291	-0.0046	0.3417	-0.0339	0.3406	21.491	67.6185	61.8962
13	0.0832	0.1016	0.1369	0.3429	0.2791	0.3808	-0.7791	-0.052	0.2119	-0.1531	-0.2683	0.3459	0.0131	0.0135	-0.0426	0.5164	-0.021	0.1021	0.3881	0.0126	0.5312	14.0709	76.2971	54.3978
14	0.5866	-0.4584	1.6029	0.5099	-1.9044	7.1855	-0.767	0.2379	-0.0612	0.285	0.0461	0.2104	-0.0945	0.5909	-0.2179	0.44	-0.0396	0.0916	0.2571	-0.0948	0.6049	16.2327	56.3546	58.0225
15	0.0061	0.0795	-0.0046	1.1254	-0.1169	0.2096	0.0529	0.5273	0.2839	-0.0951	0.0364	0.9437	-0.0578	-0.5985	0.0301	0.4332	0.0123	-0.0687	0.7252	0.0245	0.64	1.1054	75.8555	50.2631
16	0.9737	0.2103	0.7411	0.6153	-1.0084	2.7392	0.0845	-0.2275	-0.0531	0.2252	-0.1258	-0.0314	-0.5271	-0.0379	0.027	0.4043	0.0119	-0.0362	0.269	0.0218	0.3195	23.2106	87.8423	35.7078
17	0.6276	-0.4778	0.94	0.5421	-0.6881	1.405	-0.1644	0.0683	0.0696	0.0225	0.1213	0.0629	-0.0815	-0.0424	-0.005	0.3534	-0.0266	-0.0815	0.3032	0.0505	0.3846	22.0364	87.3026	21.7938
18	0.6312	0.0264	-0.3732	0.4655	0.392	1.0332	0.1171	0.1613	-0.1457	-0.3929	-0.0387	0.041	0.4192	0.111	-0.0005	0.4504	-0.0281	-0.1389	0.3336	-0.0034	0.4112	15.9972	76.9742	6.0231
19	1.1195	0.04	0.1872	0.1573	-0.4444	1.2857	-0.1093	-0.0616	0.0588	0.0405	0.1597	0.1618	-0.0255	-0.2168	0	0.303	0.0125	-0.0707	0.2817	0.0295	0.3946	16.1838	83.5643	24.2832
20	0.0801	0.0289	-0.0427	0.0867	0.0322	0.0995	0.2185	0.5685	-0.0171	-0.5245	0.0634	-0.1233	0.4309	0.3262	-0.0003	0.3965	-0.1012	-0.055	0.4251	0.012	0.4303	29.1822	88.7606	24.8759
21	9.4824	-1.9849	-2.3673	0.4157	0.4822	1.5096	-0.0635	-1.0844	0.6489	0.0258	0.2942	-0.217	0.746	0.1775	0.1851	0.6154	-0.0563	-0.1353	0.2552	-0.0698	0.3853	18.1045	74.6823	15.5403

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:24)
2	X-RAY DIFFRACTION	2	(chain A and resid 25:88)
3	X-RAY DIFFRACTION	3	(chain A and resid 89:126)
4	X-RAY DIFFRACTION	4	(chain A and resid 127:217)
5	X-RAY DIFFRACTION	5	(chain A and resid 218:259)
6	X-RAY DIFFRACTION	6	(chain A and resid 301:301)
7	X-RAY DIFFRACTION	7	(chain A and resid 302:302)
8	X-RAY DIFFRACTION	8	(chain B and resid 1:24 or chain B and resseq 305)
9	X-RAY DIFFRACTION	9	(chain B and resid 25:89)
10	X-RAY DIFFRACTION	10	(chain B and resid 90:126)
11	X-RAY DIFFRACTION	11	(chain B and resid 127:200)
12	X-RAY DIFFRACTION	12	(chain B and resid 201:259)
13	X-RAY DIFFRACTION	13	(chain B and resid 301:301)
14	X-RAY DIFFRACTION	14	(chain B and resid 302:302)
15	X-RAY DIFFRACTION	15	(chain C and resid 3:19)
16	X-RAY DIFFRACTION	16	(chain C and resid 20:87)
17	X-RAY DIFFRACTION	17	(chain C and resid 88:126)
18	X-RAY DIFFRACTION	18	(chain C and resid 127:199)
19	X-RAY DIFFRACTION	19	(chain C and resid 200:259)
20	X-RAY DIFFRACTION	20	(chain C and resid 301:301)
21	X-RAY DIFFRACTION	21	(chain C and resid 302:302)

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About Yorodumi

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Yorodumi