PDB-5j60: Structure of a thioredoxin reductase from Gloeobacter violaceus

ID or keywords:

Entry

Database: PDB / ID: 5j60

Title

Structure of a thioredoxin reductase from Gloeobacter violaceus

Components

Thioredoxin reductase

Keywords

OXIDOREDUCTASE / thioredoxin reductase

Function / homology

Function and homology information

thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Gloeobacter violaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Buey, R.M. / de Pereda, J.M. / Balsera, M.

Citation

Journal: Mol Plant / Year: 2017
Title: A New Member of the Thioredoxin Reductase Family from Early Oxygenic Photosynthetic Organisms.
Authors: Buey, R.M. / Galindo-Trigo, S. / Lopez-Maury, L. / Velazquez-Campoy, A. / Revuelta, J.L. / Florencio, F.J. / de Pereda, J.M. / Schurmann, P. / Buchanan, B.B. / Balsera, M.

History

Deposition	Apr 4, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2017	Group: Database references
Revision 1.2	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Jan 10, 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 / 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_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.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_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.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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j60.cif.gz	673.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5j60.ent.gz	564.2 KB	Display	PDB format
PDBx/mmJSON format	5j60.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5j60_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5j60_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5j60_validation.xml.gz	51.6 KB	Display
Data in CIF	5j60_validation.cif.gz	72.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j6/5j60 ftp://data.pdbj.org/pub/pdb/validation_reports/j6/5j60	HTTPS FTP

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Related structure data

Related structure data	2q7vS S: Starting model for refinement
Similar structure data	1uus-d 2e4a-2 4yjf-d 1dao-1 1xec-d 4n2q-1 2817 1evi-d 1z8u-d 1uur-d 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

2q7vS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (2) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Thioredoxin reductase

B: Thioredoxin reductase

C: Thioredoxin reductase

D: Thioredoxin reductase

hetero molecules

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

1

C: Thioredoxin reductase

hetero molecules

B: Thioredoxin reductase

hetero molecules

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

2

A: Thioredoxin reductase

D: Thioredoxin reductase

hetero molecules

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

3

B: Thioredoxin reductase

hetero molecules

C: Thioredoxin reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.278, 122.042, 139.153
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Thioredoxin reductase Mass: 34502.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria) Strain: PCC 7421 / Gene: glr0719 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7NMP6
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.56 Å³/Da / Density % sol: 51.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 30 & PEG-400 0.1 M Natrium Acetate, pH 4.5 0.2 M Calcium acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 22, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.222 Å / Num. obs: 112104 / % possible obs: 100 % / Redundancy: 13.3 % / CC_1/2: 1 / R_merge(I) obs: 0.06825 / Net I/σ(I): 24.02
Reflection shell	Resolution: 1.9→1.968 Å / Redundancy: 12.3 % / R_merge(I) obs: 1.523 / Mean I/σ(I) obs: 1.59 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2341: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2q7v

2q7v

Resolution: 1.9→49.222 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.59

	R_factor	Num. reflection	% reflection
R_free	0.2015	5592	4.99 %
R_work	0.1767	-	-
obs	0.1779	112064	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→49.222 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8949	0	240	633	9822

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	9416
X-RAY DIFFRACTION	f_angle_d	0.982	12860
X-RAY DIFFRACTION	f_dihedral_angle_d	12.714	5392
X-RAY DIFFRACTION	f_chiral_restr	0.059	1469
X-RAY DIFFRACTION	f_plane_restr	0.006	1626

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 (%)
1.9-1.9216	0.2833	166	0.2847	3477	X-RAY DIFFRACTION	100
1.9216-1.9442	0.306	180	0.2678	3569	X-RAY DIFFRACTION	100
1.9442-1.9679	0.2821	185	0.2486	3513	X-RAY DIFFRACTION	100
1.9679-1.9928	0.3029	182	0.2342	3503	X-RAY DIFFRACTION	100
1.9928-2.019	0.2564	181	0.225	3497	X-RAY DIFFRACTION	100
2.019-2.0467	0.2409	195	0.2166	3507	X-RAY DIFFRACTION	100
2.0467-2.0759	0.2536	184	0.2139	3527	X-RAY DIFFRACTION	100
2.0759-2.1069	0.2558	189	0.2053	3523	X-RAY DIFFRACTION	100
2.1069-2.1399	0.1975	163	0.1988	3539	X-RAY DIFFRACTION	100
2.1399-2.1749	0.2334	191	0.1942	3496	X-RAY DIFFRACTION	100
2.1749-2.2124	0.2048	181	0.1881	3506	X-RAY DIFFRACTION	100
2.2124-2.2527	0.2259	184	0.1832	3558	X-RAY DIFFRACTION	100
2.2527-2.296	0.236	186	0.1799	3469	X-RAY DIFFRACTION	100
2.296-2.3429	0.1912	165	0.1718	3574	X-RAY DIFFRACTION	100
2.3429-2.3938	0.2101	190	0.1661	3520	X-RAY DIFFRACTION	100
2.3938-2.4495	0.1888	207	0.1671	3519	X-RAY DIFFRACTION	100
2.4495-2.5107	0.2015	188	0.1695	3524	X-RAY DIFFRACTION	100
2.5107-2.5786	0.2059	185	0.1616	3543	X-RAY DIFFRACTION	100
2.5786-2.6545	0.1918	212	0.166	3520	X-RAY DIFFRACTION	100
2.6545-2.7402	0.1852	176	0.1697	3551	X-RAY DIFFRACTION	100
2.7402-2.8381	0.1969	193	0.1758	3560	X-RAY DIFFRACTION	100
2.8381-2.9517	0.2114	186	0.1856	3527	X-RAY DIFFRACTION	100
2.9517-3.086	0.2075	207	0.1802	3557	X-RAY DIFFRACTION	100
3.086-3.2487	0.2295	196	0.1906	3530	X-RAY DIFFRACTION	100
3.2487-3.4522	0.2361	193	0.1828	3586	X-RAY DIFFRACTION	100
3.4522-3.7187	0.1718	176	0.1683	3582	X-RAY DIFFRACTION	100
3.7187-4.0927	0.1668	199	0.1466	3606	X-RAY DIFFRACTION	100
4.0927-4.6846	0.1504	193	0.1326	3617	X-RAY DIFFRACTION	100
4.6846-5.9005	0.1694	178	0.1605	3662	X-RAY DIFFRACTION	100
5.9005-49.2381	0.2263	181	0.2069	3810	X-RAY DIFFRACTION	99

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	2.0632	0.6217	0.5375	2.7003	0.2473	1.8146	-0.0381	-0.2112	0.0741	-0.0732	0.0817	0.6401	-0.1524	-0.3764	-0.0008	0.2729	0.045	0.0381	0.2875	0.0015	0.3066	-39.2459	-0.4312	0.9997
2	1.1904	0.8597	-0.0133	0.8678	-0.2447	0.7543	0.0889	-0.3817	-0.3133	0.3903	-0.0597	-0.1113	0.0255	-0.0584	0.0001	0.3654	0.0009	0.0096	0.3857	-0.0068	0.3032	-25.5488	-3.2912	10.6354
3	1.0959	1.0955	-0.57	2.9504	0.1582	0.7304	-0.1181	0.1298	0.0303	-0.2167	0.0827	0.2651	-0.0611	-0.2087	0.0002	0.2933	-0.0012	-0.0028	0.3089	-0.0067	0.3469	-42.1763	-9.3382	-4.7167
4	2.6875	0.2502	-1.2625	3.3879	-0.4063	1.8306	-0.1855	0.2583	0.1522	-0.2573	0.1017	-0.0123	-0.1192	-0.0788	-0.0001	0.3068	-0.0292	0.0339	0.3608	-0.0207	0.3459	-46.3248	-26.0738	3.9016
5	1.6087	-0.6396	-0.4758	3.178	0.5578	1.2794	-0.4942	-0.6381	-0.4482	0.442	0.5148	-0.8015	0.2468	0.6144	-0.1254	0.3121	-0.0013	0.069	0.5615	-0.0808	0.557	-39.6513	-31.0881	12.013
6	1.0012	-0.0152	-0.4231	1.3108	-0.9701	0.7753	-0.37	0.3043	-0.526	-0.4349	0.2435	-0.1992	0.2487	-0.3496	-0.0008	0.3848	-0.0627	0.0813	0.349	-0.1149	0.4693	-40.2468	-33.4415	0.0128
7	2.8894	0.1982	0.614	1.1303	-0.0691	1.7592	-0.0486	0.2478	0.1788	-0.3571	0.1063	0.0283	-0.1391	-0.0191	-0.0005	0.3551	-0.0059	0.0221	0.2682	0.0171	0.2406	-30.1944	-0.562	-10.1678
8	1.536	-0.5267	0.4026	2.6884	-0.4362	2.3875	0.0474	0.068	0.001	-0.0841	0.0303	0.6952	0.0176	-0.285	0.0002	0.2698	-0.0202	0.0035	0.213	-0.0021	0.3744	2.5597	-14.1733	30.5372
9	1.8685	-1.0981	-0.3154	0.6906	-0.3806	1.652	-0.0612	0.7311	0.3713	-0.4085	0.0671	-0.1321	-0.1265	0.278	-0	0.3276	-0.0391	-0.0014	0.3648	0.0166	0.2872	15.761	-11.5193	20.5556
10	-0.1129	-1.1707	0.6181	2.7865	-1.2311	0.6852	-0.1413	-0.0407	0.0392	0.3946	0.1785	0.3893	-0.4214	-0.2448	0.0141	0.3937	0.0378	0.0635	0.2354	0.0029	0.4452	-1.9566	-1.0277	35.8249
11	1.4244	0.2174	1.0916	2.8006	0.0604	2.3019	-0.1052	0.2815	-0.426	-0.1395	0.1743	-0.0653	0.0865	0.0188	0.0002	0.3842	0.0235	-0.0204	0.2795	-0.0532	0.4645	-1.8869	12.0119	21.4868
12	1.6409	0.1496	0.1974	1.3905	-0.296	0.9687	0.0039	0.2625	-0.0145	0.2259	0.3073	-0.2753	-0.3643	0.2373	0.0002	0.4577	0.0419	-0.0542	0.3137	-0.0673	0.4691	-1.4514	18.2837	23.8877
13	0.846	-0.5298	-0.3627	0.8894	0.7747	0.934	0.2636	-0.1567	0.2088	0.0439	-0.009	-0.7803	-0.427	0.2782	0.0049	0.5906	0.0754	0.0057	0.311	-0.042	0.6377	0.8225	24.7988	28.3131
14	1.9284	-0.1697	0.0839	1.0843	-0.1086	1.5031	0.0289	-0.1614	0.1651	0.3198	-0.0013	0.0413	-0.1081	0.0881	0.0004	0.3697	-0.0458	0.0461	0.2357	-0.027	0.318	11.4479	-11.6653	40.4416
15	1.6916	0.2641	-0.2898	2.0979	0.3376	2.9481	0.0758	0.1841	-0.0204	0.0632	0.0297	-0.3004	0.0572	1.159	0.0843	0.1469	-0.0001	-0.0226	0.6239	-0.0261	0.2112	-47.3993	-20.0087	29.3591
16	1.6983	-0.7638	-0.4543	1.1062	-0.5684	3.4346	0.3346	-0.1749	-0.4378	1.066	-0.0843	-0.9336	1.3353	1.4671	0.6029	0.6677	0.2529	-0.2835	0.616	-0.0076	0.4227	-46.7354	-31.1884	41.8511
17	1.1758	1.048	-0.8193	1.949	-0.9488	0.5155	-0.0244	0.7882	-0.7648	-0.0953	0.4491	-0.7632	0.2606	0.4347	0.0011	0.8393	0.3146	-0.3121	0.9826	-0.3558	1.0213	-39.9512	-43.5654	30.8529
18	0.377	-0.5234	0.1303	0.6935	-0.2244	0.1275	0.2148	-0.2267	-0.5553	0.7999	1.1805	-0.2241	0.3853	-0.2208	0.0552	1.1938	0.1088	-0.2414	1.0517	-0.0442	1.0648	-43.8493	-52.1848	33.9888
19	2.8947	0.2955	0.9943	2.0735	0.6433	1.7873	0.1737	-0.2473	-0.028	0.5033	0.0563	-0.0955	0.1312	0.6805	0.2589	0.3315	0.0186	-0.0543	0.5006	-0.0552	0.2175	-51.1509	-20.9667	41.0183
20	1.9109	0.2865	0.0038	2.7092	0.4135	2.0312	-0.0776	-0.078	0.0301	0.022	0.2146	-0.4283	-0.1431	0.6029	0.0396	0.2734	-0.0677	0.0215	0.4195	-0.0727	0.3201	-6.1357	5.9709	1.8309
21	0.8921	0.6313	-0.137	0.7778	0.8925	1.5362	-0.4052	0.2855	0.1158	-0.7494	0.9341	-0.3836	-1.0229	1.0755	0.2455	0.8209	-0.4398	0.1369	0.7412	-0.1191	0.5331	-0.4352	24.4084	-4.2315
22	3.4529	-1.3044	0.3313	2.5585	-1.342	1.0909	-1.0127	-0.3099	0.8102	-0.2863	1.1848	-0.3715	-1.472	0.5269	-0.068	1.042	-0.4561	-0.1246	0.6096	-0.1157	0.4151	-2.5712	35.6942	2.6683
23	1.6241	0.7153	0.9445	1.9889	0.3579	2.3545	-0.164	0.3154	0.0336	-0.3913	0.2143	-0.0486	-0.4495	0.6448	0.0162	0.3623	-0.1205	0.1101	0.3963	-0.0486	0.2044	-10.3431	7.2773	-9.1214

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 125 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 175 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 176 through 207 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 208 through 245 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 246 through 317 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -1 through 45 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 46 through 74 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 75 through 143 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 144 through 185 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 186 through 214 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 215 through 236 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 237 through 317 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 2 through 105 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 106 through 127 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 128 through 190 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 191 through 209 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 210 through 316 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 105 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 106 through 166 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 167 through 214 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 215 through 317 )

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