PDB-5frt: Structure of the FeSII (shethna) protein of Azotobacter vinelandii

ID or keywords:

Entry

Database: PDB / ID: 5frt

Title

Structure of the FeSII (shethna) protein of Azotobacter vinelandii

Components

DIMERIC (2FE-2S) PROTEIN

Keywords

OXIDOREDUCTASE /

NITROGENASE / OXYGEN PROTECTION /

FERREDOXIN

Function / homology

Function and homology information

nitrogen fixation / 2 iron, 2 sulfur cluster binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

AZOTOBACTER VINELANDII (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.34 Å

Authors

Kabasakal, B.V. / Cotton, C.A.R. / Lieber, L. / Murray, J.W.

Citation

Journal: To be Published
Title: Structure of Fesi Protein from Azotobacter Vinelandii
Authors: Kabasakal, B. / Cotton, C.A.R. / Lieber, L. / Murray, J.W.

History

Deposition	Dec 22, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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	5frt.cif.gz	235.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5frt.ent.gz	193.4 KB	Display	PDB format
PDBx/mmJSON format	5frt.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/fr/5frt ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5frt	HTTPS FTP

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Related structure data

Related structure data	5abrC C: citing same article (ref.)
Similar structure data	5ffi-4 5ffi-1 5ffi-3 5ffi-2 5f6b-d 3il0-d 7lhn-d 5uje-d 5ld9-d 4jna-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5abrC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#26 - Feb 2002 Nitrogenase similarity (1) #117 - Sep 2009 Xanthine Oxidoreductase similarity (8) #144 - Dec 2011 Complex I similarity (5) #82 - Oct 2006 Cytochrome p450 similarity (6) #154 - Oct 2012 Citric Acid Cycle similarity (5) #111 - Mar 2009 Hydrogenase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #36 - Dec 2002 Cytochrome c similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (5)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#26 - Feb 2002
Nitrogenase
similarity (1)
#117 - Sep 2009
Xanthine Oxidoreductase
similarity (8)
#144 - Dec 2011
Complex I
similarity (5)
#82 - Oct 2006
Cytochrome p450
similarity (6)
#154 - Oct 2012
Citric Acid Cycle
similarity (5)
#111 - Mar 2009
Hydrogenase
similarity (4)
#137 - May 2011
Cytochrome bc1
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#36 - Dec 2002
Cytochrome c
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (5)

Deposited unit

A: DIMERIC (2FE-2S) PROTEIN

B: DIMERIC (2FE-2S) PROTEIN

C: DIMERIC (2FE-2S) PROTEIN

D: DIMERIC (2FE-2S) PROTEIN

E: DIMERIC (2FE-2S) PROTEIN

hetero molecules

67.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: DIMERIC (2FE-2S) PROTEIN

D: DIMERIC (2FE-2S) PROTEIN

hetero molecules

defined by author&software
26.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: DIMERIC (2FE-2S) PROTEIN

hetero molecules

B: DIMERIC (2FE-2S) PROTEIN

hetero molecules

defined by author&software
26.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: DIMERIC (2FE-2S) PROTEIN

hetero molecules

A: DIMERIC (2FE-2S) PROTEIN

hetero molecules

defined by author&software
26.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: DIMERIC (2FE-2S) PROTEIN

hetero molecules

defined by author&software
13.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	133.560, 134.530, 36.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	E-2001- HOH

#1: Protein	DIMERIC (2FE-2S) PROTEIN / FESII PROTEIN / SHETHA PROTEIN II Mass: 13289.330 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: FE2S2 CLUSTER BOUND / Source: (gene. exp.) AZOTOBACTER VINELANDII (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): KRX / References: UniProt: Q44501
#2: Chemical	ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster Mass: 175.820 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe₂S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.47 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	pH: 8 Details: 0.1M NA HEPES PH 8.0, 0.2 M NA CITRATE, 24% W/V PEG 3350.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97625, 1.73487

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97625	1
2	1.73487	1

Reflection

Resolution: 2.34→67.26 Å / Num. obs: 28854 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / B_iso Wilson estimate: 53.23 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 15.3

Reflection shell

Resolution: 2.34→2.4 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.99 / Mean I/σ(I) obs: 1.4 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX	AUTOSOL	phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.34→67.265 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2517	1341	4.7 %
R_work	0.2171	-	-
obs	0.2188	28796	99.82 %

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.34→67.265 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4353	0	20	52	4425

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4456
X-RAY DIFFRACTION	f_angle_d	1.205	5995
X-RAY DIFFRACTION	f_dihedral_angle_d	16.1	2742
X-RAY DIFFRACTION	f_chiral_restr	0.085	707
X-RAY DIFFRACTION	f_plane_restr	0.008	779

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 (%)
2.34-2.4237	0.3547	136	0.3165	2666	X-RAY DIFFRACTION	99
2.4237-2.5207	0.3555	135	0.3212	2669	X-RAY DIFFRACTION	100
2.5207-2.6354	0.3521	121	0.2925	2733	X-RAY DIFFRACTION	100
2.6354-2.7744	0.3138	129	0.2761	2701	X-RAY DIFFRACTION	100
2.7744-2.9482	0.2848	120	0.2593	2713	X-RAY DIFFRACTION	100
2.9482-3.1758	0.3128	129	0.2668	2736	X-RAY DIFFRACTION	100
3.1758-3.4954	0.2278	140	0.2221	2731	X-RAY DIFFRACTION	100
3.4954-4.0012	0.2367	121	0.2113	2782	X-RAY DIFFRACTION	100
4.0012-5.0408	0.2196	162	0.1685	2765	X-RAY DIFFRACTION	100
5.0408-67.2928	0.229	148	0.1906	2959	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	2.2074	-1.162	1.6362	3.1982	0.8934	1.0016	0.3353	0.1752	-0.4448	0.1289	-0.0584	-0.1068	0.1661	0.0985	0.0008	0.4502	-0.038	-0.0629	0.3271	-0.0273	0.4077	19.1482	-39.813	-1.6496
2	0.4217	0.4127	-0.0844	-0.5911	-1.9656	1.6038	-0.0411	0.0231	0.1629	0.4177	-0.0476	0.1319	0.0868	-0.5855	0.0001	0.6997	-0.0963	0.0201	0.4774	-0.0552	0.4711	23.1839	-15.2614	-16.2617
3	0.8749	0.9262	0.9465	1.7186	0.9798	0.3891	-0.0307	0.1239	-0.3214	-0.1778	-0.1775	-0.2042	0.0408	-0.1872	-0.0002	0.4272	0.0072	0.0128	0.4332	-0.0603	0.3631	18.2932	-35.4523	-5.507
4	1.1561	-0.2414	0.4621	0.6809	0.5536	0.7008	-0.2103	-0.0587	-0.2835	-0.4578	0.6592	-1.1327	0.0483	0.2417	0.0297	0.5007	-0.0779	0.0563	0.4516	-0.1129	0.5414	33.6238	-22.1721	-4.0294
5	-0.0213	0.0449	0.0146	-0.0146	-0.0717	-0.0522	-0.2272	-0.6801	0.4644	0.6323	0.3984	-0.3262	-0.2379	-0.1949	-0.0002	0.5112	0.1887	-0.1729	0.8487	-0.1755	0.6047	42.5781	-22.3298	11.6358
6	0.0029	-0.0031	-0.1478	0.035	0.1328	-0.0454	-0.0314	-0.0291	-0.3995	-0.2709	0.5193	-1.3876	-1.2523	0.228	0.0047	0.5588	-0.0811	0.0855	0.485	-0.2253	0.869	40.4901	-16.7509	3.3529
7	0.9472	-0.0726	0.8915	0.6205	-0.3824	0.5061	-0.1944	-0.0044	0.3634	-0.1617	0.3282	-0.3901	0.3568	0.0457	0.0002	0.4602	-0.0815	-0.0188	0.4003	-0.1192	0.51	33.5453	-11.4073	5.4578
8	0.0589	-0.5283	-0.2133	0.0758	-0.2727	-0.0169	-0.1905	-1.2279	0.2754	0.2538	0.1169	0.1056	0.1363	0.7505	-0.0007	0.713	0.0381	0.0033	0.6734	-0.1065	0.4565	21.0584	-30.7328	13.9044
9	0.0791	0.1598	0.1224	0.1527	0.1898	0.224	0.3438	0.798	-0.1192	-1.8212	0.1222	-0.8364	-0.5951	-0.589	-0.0257	0.7705	0.0437	-0.074	0.7755	-0.0239	0.7673	7.7024	-33.6052	21.0401
10	0.2829	0.2971	-0.7969	0.4181	-0.4836	1.7738	0.7442	0.2045	1.2394	0.093	1.252	1.2458	-1.9989	-0.6257	0.201	0.8643	0.0677	0.0631	0.8418	0.0012	0.8006	10.2238	-25.1943	20.9867
11	-0.1349	-0.0384	0.3701	-0.003	-0.4885	-0.1393	0.1546	0.1553	0.4977	0.8649	0.0666	0.1132	0.3213	-0.0396	0.0016	0.5481	-0.0778	0.0147	0.5069	-0.0368	0.3997	22.7233	-19.8122	8.5134
12	0.621	0.4378	0.8985	0.4719	0.77	0.2975	-0.0835	-0.2322	-0.007	-0.024	0.2083	-0.4752	0.2314	-0.4049	0.0025	0.4402	0.0361	-0.1045	0.3351	-0.0455	0.5013	31.3206	-19.0835	4.3904
13	2.7808	1.5448	-1.1269	1.289	0.5734	1.2575	0.1802	0.1471	0.9388	0.1737	-0.0244	-0.0218	-0.4279	-0.6024	0.0233	0.4378	0.2199	0.0903	0.4799	0.0184	0.5945	14.0106	26.2341	-3.2695
14	0.2513	-0.4527	-0.7111	0.8116	0.0126	0.3491	0.1659	0.5113	-0.1285	-0.5278	0.1318	0.3343	0.1188	-0.6573	0.0023	0.5602	0.0187	-0.0803	0.6203	-0.0944	0.6838	25.4598	3.6111	12.9767
15	1.3448	-0.3014	-0.6995	0.8723	-0.5235	2.149	0.1804	-0.5856	0.5622	0.3059	0.0603	0.1588	-0.0151	-0.5414	0.0001	0.5547	0.0453	0.0073	0.6836	-0.059	0.5953	14.0825	21.0727	-1.6376
16	0.5339	-0.3916	-0.2838	0.4212	0.8178	0.6832	0.2339	-0.2722	0.5784	-0.008	0.1698	0.0118	-0.2989	0.6083	0.0001	0.4833	-0.0032	0.0095	0.4114	-0.0422	0.3986	31.5923	18.6594	33.3694
17	0.1508	-0.0583	-0.1541	0.0538	0.1114	0.0435	0.762	1.4457	-0.0076	0.1328	-1.7828	0.7644	-0.0625	0.1302	-0.0002	0.7577	0.113	0.0242	0.6557	0.2385	0.5002	39.2898	23.1081	19.5629
18	0.452	-0.1807	-0.2017	0.1615	0.0432	0.125	0.5596	0.7314	0.669	-0.1854	-0.1251	-0.9877	0.5196	1.3844	-0.0174	0.4248	0.0587	0.0324	0.5538	-0.0625	0.6421	40.081	16.4383	25.8783
19	1.0155	0.6499	-0.7345	0.6075	0.125	0.7112	0.0519	0.3463	-0.3007	0.3333	0.0863	-0.5212	0.2774	0.0957	-0.0005	0.4008	0.073	-0.0784	0.5002	-0.1342	0.4674	35.9224	8.5753	24.2099
20	0.7017	1.1199	0.6392	2.988	-0.1552	1.2393	-0.2742	0.9756	-0.2871	0.8246	0.6675	0.2372	-0.3449	-0.6214	0.6711	0.0914	-0.0739	0.1741	1.1768	-0.0153	0.3358	9.8859	17.0315	10.5835
21	3.6212	1.038	-0.1461	1.4794	-0.3973	0.7213	0.0312	0.5825	-1.5969	-0.3651	-0.1225	-0.2767	-0.6984	-0.4987	-0.1031	0.4263	0.1103	-0.0928	0.6295	-0.0678	0.2097	23.4946	11.6197	20.602
22	2.3061	0.0677	-0.0875	0.0328	0.3953	0.5589	0.0934	-0.0166	-0.3519	-0.088	-0.035	-0.2915	-0.4032	-0.2422	-0.0055	0.6099	0.0371	0.0584	0.3218	0.104	0.4161	30.7564	14.7761	24.9025
23	2.8768	-0.8909	0.2015	2.5393	-0.6549	4.8605	-0.4207	-1.021	1.1369	0.0139	-0.323	0.3359	-0.2588	-0.2248	-1.3536	0.369	0.068	-0.0566	0.5977	-0.1356	0.5167	57.5322	6.7738	16.0927
24	-0.0217	-0.0591	0.1612	0.1581	0.0233	-0.1122	0.0764	-0.267	0.9424	0.38	0.7786	0.7212	0.8102	0.6472	0.003	0.5122	0.033	-0.1246	0.8651	-0.0476	1.1268	48.8508	13.2497	10.6661
25	0.8557	0.6555	-0.3499	0.3635	-0.0952	0.3165	0.0831	-0.5964	-0.0632	-0.0632	0.228	0.6119	0.4648	-0.6073	0.0175	0.2849	0.0359	-0.0374	0.5733	0.0945	0.4342	53.7565	2.5314	6.5663
26	0.2722	-0.2373	-0.4646	0.0943	0.459	0.8998	0.2417	0.3131	-0.2633	0.5599	-0.5176	-0.7468	0.3021	-0.4028	-0.1561	0.716	0.1046	-0.1398	0.6312	0.2156	0.8037	50.444	-9.4661	9.6514
27	1.48	2.0272	0.0236	0.8546	-0.4379	0.1084	-0.6419	0.0388	0.2569	-0.23	0.5167	0.2186	0.0932	-0.0427	-0.0625	0.3815	-0.0344	-0.0863	0.5203	0.0346	0.4294	52.2215	1.173	4.9926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 2 THROUGH 56 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 57 THROUGH 96 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 97 THROUGH 120 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 2 THROUGH 18 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 19 THROUGH 26 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 27 THROUGH 33 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 34 THROUGH 56 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 57 THROUGH 68 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 69 THROUGH 77 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 78 THROUGH 89 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 90 THROUGH 103 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 104 THROUGH 120 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 2 THROUGH 68 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 69 THROUGH 89 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 90 THROUGH 120 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 2 THROUGH 18 )
17	X-RAY DIFFRACTION	17	CHAIN 'D' AND (RESID 19 THROUGH 26 )
18	X-RAY DIFFRACTION	18	CHAIN 'D' AND (RESID 27 THROUGH 33 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 34 THROUGH 56 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 57 THROUGH 89 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 90 THROUGH 103 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 104 THROUGH 120 )
23	X-RAY DIFFRACTION	23	CHAIN 'E' AND (RESID 2 THROUGH 33 )
24	X-RAY DIFFRACTION	24	CHAIN 'E' AND (RESID 34 THROUGH 43 )
25	X-RAY DIFFRACTION	25	CHAIN 'E' AND (RESID 44 THROUGH 58 )
26	X-RAY DIFFRACTION	26	CHAIN 'E' AND (RESID 59 THROUGH 68 )
27	X-RAY DIFFRACTION	27	CHAIN 'E' AND (RESID 69 THROUGH 120 )

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