PDB-5k0a: Structure of an oxidoreductase from Synechocystis sp. PCC6803

ID or keywords:

Entry

Database: PDB / ID: 5k0a

Title

Structure of an oxidoreductase from Synechocystis sp. PCC6803

Components

Slr0600 protein

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

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

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.706 Å

Authors

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

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unprecedented pathway of reducing equivalents in a diflavin-linked disulfide oxidoreductase.
Authors: Buey, R.M. / Arellano, J.B. / Lopez-Maury, L. / Galindo-Trigo, S. / Velazquez-Campoy, A. / Revuelta, J.L. / de Pereda, J.M. / Florencio, F.J. / Schurmann, P. / Buchanan, B.B. / Balsera, M.

History

Deposition	May 17, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Sep 8, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Jan 10, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5k0a.cif.gz	752.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5k0a.ent.gz	637.1 KB	Display	PDB format
PDBx/mmJSON format	5k0a.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/k0/5k0a ftp://data.pdbj.org/pub/pdb/validation_reports/k0/5k0a	HTTPS FTP

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Related structure data

Related structure data	5jriSC 5n0jC 5odeC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5jri-d 6bpy-d 5ode-d 4jn9-d 6eh1-d 4ntc-d 4usm-2 7br0-1 4nte-d 3tpz-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) 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	#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: Slr0600 protein

B: Slr0600 protein

C: Slr0600 protein

D: Slr0600 protein

hetero molecules

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

1

A: Slr0600 protein

B: Slr0600 protein

hetero molecules

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

2

C: Slr0600 protein

D: Slr0600 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.029, 128.430, 92.728
Angle α, β, γ (deg.)	90.00, 91.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Slr0600 protein Mass: 36464.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Cys159 has modelled as cystein sulfenic acid (Cys-SOH; CSO) Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr0600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74746

#1: Protein

Slr0600 protein

Mass: 36464.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cys159 has modelled as cystein sulfenic acid (Cys-SOH; CSO)
Source: (gene. exp.)

Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr0600 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74746

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Non-polymers , 7 types, 1230 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO₄
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1200 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.69 Å³/Da / Density % sol: 54.35 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.03 M NaNO3 0.03 M PO4H2Na 0.03 M (NH4)2SO4 0.1 M Imidazole/Mes, pH 6.5 20% (v/v) PEG-500 MME 10% (w/v) PEG-20000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99987 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 1.706→49.043 Å / Num. obs: 167283 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.09973 / Net I/σ(I): 10.66
Reflection shell	Resolution: 1.706→1.767 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.298 / Mean I/σ(I) obs: 1.08 / % 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: 5JRI

5jri

Resolution: 1.706→49.042 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 24.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1926	16334	4.93 %
R_work	0.165	-	-
obs	0.1664	167233	99.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.706→49.042 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9783	0	634	1200	11617

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10656
X-RAY DIFFRACTION	f_angle_d	1.413	14504
X-RAY DIFFRACTION	f_dihedral_angle_d	14.086	5941
X-RAY DIFFRACTION	f_chiral_restr	0.197	1612
X-RAY DIFFRACTION	f_plane_restr	0.005	1759

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 (%)
1.7055-1.7249	0.3639	526	0.3692	10120	X-RAY DIFFRACTION	96
1.7249-1.7452	0.3578	556	0.3389	10548	X-RAY DIFFRACTION	100
1.7452-1.7665	0.355	492	0.3291	10438	X-RAY DIFFRACTION	100
1.7665-1.7888	0.3519	526	0.3303	10582	X-RAY DIFFRACTION	100
1.7888-1.8124	0.3437	483	0.3152	10551	X-RAY DIFFRACTION	100
1.8124-1.8372	0.3248	587	0.3103	10509	X-RAY DIFFRACTION	100
1.8372-1.8634	0.3393	522	0.3096	10428	X-RAY DIFFRACTION	100
1.8634-1.8913	0.3264	534	0.2989	10637	X-RAY DIFFRACTION	100
1.8913-1.9208	0.3383	532	0.2996	10453	X-RAY DIFFRACTION	100
1.9208-1.9523	0.3298	477	0.298	10573	X-RAY DIFFRACTION	100
1.9523-1.986	0.3087	456	0.2631	10537	X-RAY DIFFRACTION	100
1.986-2.0221	0.2567	506	0.2349	10551	X-RAY DIFFRACTION	100
2.0221-2.061	0.247	535	0.2177	10591	X-RAY DIFFRACTION	100
2.061-2.103	0.255	548	0.1985	10465	X-RAY DIFFRACTION	100
2.103-2.1488	0.2119	581	0.1769	10472	X-RAY DIFFRACTION	100
2.1488-2.1988	0.2097	579	0.162	10468	X-RAY DIFFRACTION	100
2.1988-2.2537	0.2099	506	0.1629	10558	X-RAY DIFFRACTION	100
2.2537-2.3147	0.1902	528	0.1515	10490	X-RAY DIFFRACTION	100
2.3147-2.3828	0.1934	639	0.1415	10416	X-RAY DIFFRACTION	100
2.3828-2.4597	0.183	590	0.1393	10488	X-RAY DIFFRACTION	100
2.4597-2.5476	0.1771	540	0.139	10498	X-RAY DIFFRACTION	100
2.5476-2.6496	0.1863	590	0.1421	10502	X-RAY DIFFRACTION	100
2.6496-2.7702	0.1905	492	0.1474	10541	X-RAY DIFFRACTION	100
2.7702-2.9162	0.1729	603	0.1445	10438	X-RAY DIFFRACTION	100
2.9162-3.0989	0.1759	581	0.1507	10475	X-RAY DIFFRACTION	100
3.0989-3.3381	0.1699	520	0.1488	10550	X-RAY DIFFRACTION	100
3.3381-3.6739	0.1739	549	0.1395	10500	X-RAY DIFFRACTION	100
3.6739-4.2053	0.1384	624	0.1204	10402	X-RAY DIFFRACTION	100
4.2053-5.2972	0.1398	557	0.1126	10445	X-RAY DIFFRACTION	100
5.2972-49.0625	0.1673	575	0.1595	10464	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	0.8438	0.0474	0.1573	0.9706	0.182	1.6213	-0.0082	-0.1051	0.1538	0.0164	-0.0308	0.0429	-0.2159	-0.3009	-0	0.2802	0.0719	-0.011	0.1997	-0.031	0.2443	-12.8716	28.9074	-16.4221
2	0.531	-0.1516	-0.091	0.5288	-0.4813	0.5442	0.0584	-0.2119	-0.1204	0.2128	0.007	0.0773	0.2133	-0.4019	-0	0.2945	0.0298	0.0153	0.4295	-0.0664	0.3023	-24.5127	21.2136	-5.8517
3	1.537	0.1202	0.597	0.2505	0.2252	0.9723	-0.022	-0.1375	0.0503	0.0251	0.0044	-0.0563	0.0021	-0.0031	-0.0004	0.2701	0.0239	0.0039	0.1837	-0.0086	0.2519	2.5219	21.5809	-8.3469
4	0.9014	0.3606	0.2601	0.2752	0.1228	1.9162	-0.0239	0.2484	0.122	-0.1039	0.0138	-0.064	-0.2394	0.2704	-0.0023	0.3286	-0.0475	0.0228	0.2104	0.033	0.2664	10.7116	27.7851	-32.7253
5	0.4254	0.2179	0.0366	0.4343	0.3574	0.3634	-0.0462	0.4447	-0.0214	-0.2964	0.0898	-0.2266	0.1087	0.3197	0.0001	0.4116	-0.0294	0.1229	0.5895	-0.0148	0.3868	21.4171	21.4543	-44.1993
6	0.3014	0.1176	-0.2535	0.6047	0.3277	0.5755	-0.0529	0.3026	0.1309	-0.2245	-0.0293	-0.0598	-0.2107	0.2188	-0.0001	0.3711	-0.0388	0.0567	0.2955	0.0274	0.2773	4.4926	24.5351	-45.2369
7	0.6252	0.054	0.0785	0.4652	-0.4663	0.5455	-0.047	0.0899	0.0559	-0.1623	-0.0691	-0.123	-0.3139	-0.157	0.001	0.3942	0.0521	-0.0264	0.3434	-0.0099	0.2787	-16.8437	24.9561	-43.2255
8	0.5369	0.2171	0.2962	0.5617	-0.1449	0.3338	-0.0985	0.1508	-0.1712	-0.3345	0.0151	0.0085	-0.1248	-0.1649	-0.0002	0.3497	0.0387	-0.0232	0.3791	-0.0365	0.2504	-23.0469	18.2364	-52.4658
9	1.0102	0.0606	0.4921	0.3108	0.2812	1.0917	-0.0105	0.1213	-0.042	-0.1384	0.0166	-0.0252	-0.094	0.0476	-0	0.3178	-0.0087	0.0349	0.2072	0.0037	0.2566	2.3171	19.6473	-35.7398
10	0.8596	-0.1667	0.0046	0.2734	-0.0853	1.1135	0.027	0.1397	-0.1115	0.0004	-0.015	-0.0589	0.1557	0.1514	0	0.2141	0.0355	0.0009	0.258	-0.0412	0.2564	-22.1867	51.6426	-26.24
11	0.6697	0.3421	0.0609	0.6845	0.6809	0.8298	-0.0887	0.1966	0.015	0.0669	0.0667	-0.1863	-0.1388	0.2081	-0.0001	0.2216	0.0527	0.0434	0.4217	0.0063	0.2845	-7.3436	57.1219	-35.2826
12	0.4974	0.1331	-0.1922	0.5796	0.2803	0.33	0.0438	0.1125	-0.1339	0.077	-0.0223	-0.0875	0.2021	0.1805	0	0.2112	0.0258	0.0038	0.2714	-0.0216	0.2891	-11.8358	53.9422	-13.503
13	0.9075	-0.5408	-0.3286	0.9111	0.0516	1.1262	0.0331	-0.1289	0.0758	0.0983	0.0059	-0.1121	-0.017	0.0554	0.0005	0.2412	0.0019	-0.0229	0.2173	-0.0121	0.2375	-18.7265	59.5098	4.7144
14	0.3908	-0.0252	-0.234	0.1517	-0.0261	0.2968	-0.0217	-0.2636	-0.2664	0.1762	0.0758	-0.1486	0.2153	0.0027	0.0069	0.3652	0.0332	-0.0543	0.2843	0.0227	0.3307	-13.662	48.1482	6.0803
15	0.2979	-0.0216	-0.1186	0.079	-0.0406	0.1189	-0.0129	0.1843	0.1581	0.0616	0.0431	-0.1423	-0.3034	0.305	0.0001	0.3029	-0.0384	0.0087	0.348	0.0163	0.3162	-11.6813	67.2119	-20.7289
16	1.004	0.5144	0.0576	1.116	0.2149	0.2026	-0.049	0.1797	0.0701	-0.019	0.0051	-0.0154	-0.285	0.1406	-0.0101	0.1793	0.0127	0.0277	0.2672	0.0124	0.2117	-27.02	65.3033	-31.8113
17	1.0373	-0.1185	0.4107	0.5963	0.2032	1.3035	0.0217	-0.0635	-0.0612	0.0425	-0.0298	0.0822	0.094	-0.112	0.0001	0.1933	-0.0178	0.0118	0.1962	0.0061	0.2408	-45.6693	55.9697	-12.4732
18	0.5659	-0.3079	-0.2339	0.5577	-0.3941	0.7905	-0.0387	-0.0947	0.202	-0.0618	-0.0257	0.146	-0.1447	-0.1583	0	0.2319	-0.0091	0.0262	0.3194	-0.042	0.2845	-58.9391	65.4398	-7.0253
19	0.4302	-0.0432	-0.121	0.3885	-0.1714	0.2738	0.0186	0.024	0.0238	-0.0226	-0.0637	0.0929	0.0951	-0.191	0.0001	0.2024	0.0169	0.0145	0.2792	-0.0141	0.2635	-53.9108	60.5276	-23.0542
20	0.7497	0.5518	0.1081	0.7175	-0.1315	1.0746	0.019	0.1541	0.0043	0.0234	0.012	0.1219	-0.0694	0.0439	-0.0009	0.2445	0.0224	-0.005	0.2756	-0.0007	0.2275	-45.4982	58.5869	-43.3026
21	0.2019	-0.2421	-0.0252	0.3299	0.1415	0.3077	0.0562	0.1112	0.0565	-0.1412	-0.0187	0.2016	-0.173	0.056	-0.0001	0.2975	0.0179	-0.0356	0.2983	0.0146	0.2657	-51.0158	62.6759	-52.0444
22	0.6	-0.1086	0.1268	0.3805	-0.3593	0.5241	0.0273	0.1038	-0.1224	-0.1501	-0.0048	0.1218	0.115	-0.1074	-0.0001	0.2637	0.0043	-0.0105	0.2735	-0.0114	0.2881	-52.9024	55.9951	-38.9423
23	0.7796	-0.391	-0.2793	1.2493	0.0646	0.4077	0.0305	0.0568	0.1242	-0.0626	-0.0384	0.0216	-0.297	0.0595	-0.001	0.1977	-0.0066	0.0276	0.1963	-0.002	0.2385	-37.7058	69.1772	-11.2497

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 101 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 102 through 120 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 121 through 330 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 10 through 101 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 102 through 120 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 121 through 147 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 148 through 188 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 189 through 222 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 223 through 330 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 18 through 101 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 102 through 124 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 125 through 147 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 148 through 222 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 223 through 252 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 253 through 272 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 273 through 330 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 9 through 101 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 102 through 120 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 121 through 147 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 148 through 204 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 205 through 227 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 228 through 262 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 263 through 330 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 7 types, 1230 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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Aug 12, 2020. Covid-19 info

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

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Yorodumi