PDB-5jri: Structure of an oxidoreductase SeMet-labelled from Synechocystis ...

ID or keywords:

Entry

Database: PDB / ID: 5jri

Title

Structure of an oxidoreductase SeMet-labelled from Synechocystis sp. PCC6803

Components

Pyridine nucleotide-disulfide oxidoreductase

Keywords

OXIDOREDUCTASE

Function / homology

thioredoxin-disulfide reductase (NADPH) activity / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / cell redox homeostasis / FAD/NAD(P)-binding domain superfamily /

FLAVIN-ADENINE DINUCLEOTIDE /

: / Slr0600 protein

Function and homology information

Biological species

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.952 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 6, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5jri.cif.gz	365.9 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	5k0aC 5n0jC 5odeC C: citing same article (ref.)
Similar structure data	5k0a-2 5k0a-1 6bpy-d 4nte-d 4fk1-1 3fbs-2 3f8p-2 4jna-d 4jn9-d 3f8r-1 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: Pyridine nucleotide-disulfide oxidoreductase

B: Pyridine nucleotide-disulfide oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	71.734, 79.327, 127.049
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pyridine nucleotide-disulfide oxidoreductase Mass: 36964.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: All Met residues substituted by SeMet / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: AOY38_16435 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0GNW3, UniProt: P74746*PLUS
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.48 Å³/Da / Density % sol: 50.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM Bis-tris propane, pH 7.5 200 mM Na2SO4 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97922 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97922 Å / Relative weight: 1
Reflection	Resolution: 1.952→49.08 Å / Num. obs: 101579 / % possible obs: 100 % / Redundancy: 6.7 % / R_merge(I) obs: 0.2378 / Net I/σ(I): 5.94
Reflection shell	Resolution: 1.952→2.022 Å / Redundancy: 5.6 % / R_merge(I) obs: 1.5446 / Mean I/σ(I) obs: 1 / % possible all: 99

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.952→49.08 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 28.79

	R_factor	Num. reflection	% reflection
R_free	0.2421	5082	5.01 %
R_work	0.1991	-	-
obs	0.2012	101446	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.952→49.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4807	0	274	421	5502

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5185
X-RAY DIFFRACTION	f_angle_d	1.302	7094
X-RAY DIFFRACTION	f_dihedral_angle_d	10.29	2864
X-RAY DIFFRACTION	f_chiral_restr	0.155	789
X-RAY DIFFRACTION	f_plane_restr	0.004	860

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 (%)
1.9525-1.9747	0.3936	164	0.3723	3167	X-RAY DIFFRACTION	97
1.9747-1.9979	0.3691	155	0.3358	3215	X-RAY DIFFRACTION	100
1.9979-2.0223	0.3799	200	0.3369	3157	X-RAY DIFFRACTION	100
2.0223-2.0478	0.3264	134	0.3149	3241	X-RAY DIFFRACTION	100
2.0478-2.0748	0.3161	172	0.2881	3208	X-RAY DIFFRACTION	100
2.0748-2.1032	0.2955	217	0.2672	3172	X-RAY DIFFRACTION	100
2.1032-2.1333	0.2599	173	0.2629	3165	X-RAY DIFFRACTION	100
2.1333-2.1651	0.3159	184	0.2517	3218	X-RAY DIFFRACTION	100
2.1651-2.1989	0.3018	193	0.2338	3211	X-RAY DIFFRACTION	100
2.1989-2.235	0.264	193	0.2372	3191	X-RAY DIFFRACTION	100
2.235-2.2735	0.2843	179	0.2209	3209	X-RAY DIFFRACTION	100
2.2735-2.3149	0.2977	168	0.2233	3224	X-RAY DIFFRACTION	100
2.3149-2.3594	0.2678	189	0.2304	3161	X-RAY DIFFRACTION	100
2.3594-2.4076	0.3339	181	0.2157	3235	X-RAY DIFFRACTION	100
2.4076-2.4599	0.2917	164	0.2152	3186	X-RAY DIFFRACTION	100
2.4599-2.5171	0.2776	153	0.2238	3230	X-RAY DIFFRACTION	100
2.5171-2.5801	0.2772	149	0.2298	3235	X-RAY DIFFRACTION	100
2.5801-2.6498	0.2721	193	0.2193	3227	X-RAY DIFFRACTION	100
2.6498-2.7278	0.317	143	0.2288	3265	X-RAY DIFFRACTION	100
2.7278-2.8158	0.2921	149	0.2282	3218	X-RAY DIFFRACTION	100
2.8158-2.9165	0.3135	153	0.2239	3224	X-RAY DIFFRACTION	100
2.9165-3.0332	0.2446	167	0.2173	3237	X-RAY DIFFRACTION	100
3.0332-3.1712	0.2126	149	0.2032	3242	X-RAY DIFFRACTION	100
3.1712-3.3384	0.2553	152	0.1851	3216	X-RAY DIFFRACTION	100
3.3384-3.5475	0.2195	175	0.1669	3209	X-RAY DIFFRACTION	100
3.5475-3.8213	0.18	177	0.1537	3229	X-RAY DIFFRACTION	100
3.8213-4.2057	0.1294	162	0.13	3203	X-RAY DIFFRACTION	100
4.2057-4.8138	0.1831	163	0.1179	3236	X-RAY DIFFRACTION	100
4.8138-6.0632	0.19	193	0.1515	3190	X-RAY DIFFRACTION	100
6.0632-49.6011	0.1826	138	0.195	3243	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	0.7425	-0.1839	-0.2304	0.3537	-0.0339	0.2956	0.0055	-0.051	0.0258	0.0154	-0.038	-0.0238	0.0438	0.0407	0.0008	0.2434	-0.0038	-0.0068	0.2584	-0.0184	0.2644	29.7827	37.7418	-5.6029
2	0.5184	-0.3546	-0.0273	0.2541	0.1391	1.1632	0.0131	0.1232	0.094	-0.044	-0.0365	-0.009	-0.2186	0.142	0.0001	0.291	-0.0286	-0.0108	0.3414	0.0147	0.2879	41.8688	42.9042	22.0148
3	0.2214	-0.0393	0.083	0.0895	-0.0993	0.1156	-0.0754	-0.1597	0.0899	0.1079	0.0518	-0.1474	-0.1247	0.1345	-0	0.325	-0.0145	-0.0088	0.3829	0.0284	0.3484	45.3526	35.1378	18.5466
4	0.4334	0.3898	0.1512	0.5782	0.3623	0.2666	0.0102	-0.2337	0.1098	0.0232	-0.0564	0.0433	-0.068	-0.1929	-0	0.2523	-0.0087	-0.0086	0.2384	-0.0047	0.2303	21.1306	50.4612	-6.2248
5	0.2498	-0.0244	-0.1117	0.2313	-0.0837	0.17	-0.0146	-0	-0.1192	-0.0111	-0.0296	0.0659	0.0987	-0.1477	-0	0.237	-0.0029	-0.0058	0.2651	0.0222	0.2456	11.0279	36.7988	13.9757
6	0.6715	0.0139	0.1151	0.692	-0.5728	0.7307	0.0214	-0.1551	0.0696	0.1745	-0.0507	0.1458	0.071	-0.2193	-0.0001	0.2285	-0.0159	0.0038	0.2936	-0.0142	0.2404	5.4496	38.4976	23.9558
7	0.3272	-0.1735	-0.2293	0.6699	-0.0649	0.2857	0.1369	-0.2144	0.0727	0.0592	-0.2492	0.1836	0.1697	-0.2697	-0.005	0.2593	-0.0013	0.0328	0.2893	-0.0051	0.2526	-2.8057	40.3117	12.5233
8	0.579	0.2439	0.0716	0.2365	-0.2269	1.245	0.0704	-0.0641	0.1143	0.0469	-0.11	0.0642	-0.0815	-0.0901	0	0.2792	0.0063	0.0018	0.3325	-0.0193	0.3179	-7.0886	40.1033	-10.4635
9	0.3426	-0.1929	-0.1118	0.4485	-0.2822	0.3923	-0.0046	0.3663	0.001	-0.0365	0.0529	0.262	0.2065	-0.1522	0	0.3101	0.046	-0.0117	0.2676	-0.0021	0.3184	-0.5286	52.394	13.4322
10	0.4703	-0.2953	-0.0245	0.5144	-0.356	0.4089	-0.0557	0.1375	0.1405	-0.0136	-0.0334	-0.0253	-0.1976	0.059	-0	0.2737	-0.0031	-0.0041	0.3027	0.01	0.2451	18.1359	49.858	17.339

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 147 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 148 through 227 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 228 through 257 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 258 through 330 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 72 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 73 through 120 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 121 through 147 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 148 through 252 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 253 through 272 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 273 through 330 )

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