PDB-5ode: Structure of a novel oxidoreductase from Gloeobacter violaceus

ID or keywords:

Entry

Database: PDB / ID: 5ode

Title

Structure of a novel oxidoreductase from Gloeobacter violaceus

Components

Gll2934 protein

Keywords

OXIDOREDUCTASE / flavoprotein

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 / Gll2934 protein

Function and homology information

Biological species

Gloeobacter violaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.196 Å

Authors

Buey, R.M. / Galindo-Trigo, S. / 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	Jul 5, 2017	Deposition site: PDBE / 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	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ode.cif.gz	380.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ode.ent.gz	318.7 KB	Display	PDB format
PDBx/mmJSON format	5ode.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ode_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5ode_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5ode_validation.xml.gz	30.5 KB	Display
Data in CIF	5ode_validation.cif.gz	41.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/od/5ode ftp://data.pdbj.org/pub/pdb/validation_reports/od/5ode	HTTPS FTP

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Related structure data

Related structure data	5jriSC 5k0aC 5n0jC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5k0a-1 4jn9-d 6eh1-d 5jri-d 5k0a-2 2qjw-d 1tf0-d 6bpy-d 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: Gll2934 protein

B: Gll2934 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.229, 136.419, 267.676
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Gll2934 protein Mass: 38833.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: gll2934 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7NCP4
#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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.62 Å³/Da / Density % sol: 66.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5 1.5 M Lis2SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.99986 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99986 Å / Relative weight: 1
Reflection	Resolution: 2.195→60.772 Å / Num. obs: 38467 / % possible obs: 96.4 % / Redundancy: 12.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.031 / Net I/σ(I): 16.8
Reflection shell	Resolution: 2.195→2.27 Å / Redundancy: 11.4 % / R_merge(I) obs: 1.031 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1912 / CC_1/2: 0.77 / R_pim(I) all: 0.325 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.12rc1_2801: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JRI

5jri

Resolution: 2.196→60.772 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.76
Details: STARANISO truncated data was used for refinement to correct for anisotropy. These truncated data has 2.20 and 3.23 A as best and worst-resolution limits, respectively. The deposited file ...

	R_factor	Num. reflection	% reflection
R_free	0.2658	1972	5.13 %
R_work	0.2463	-	-
obs	0.2473	38442	71.02 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.196→60.772 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4965	0	267	262	5494

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5362
X-RAY DIFFRACTION	f_angle_d	0.552	7316
X-RAY DIFFRACTION	f_dihedral_angle_d	15.466	3000
X-RAY DIFFRACTION	f_chiral_restr	0.044	796
X-RAY DIFFRACTION	f_plane_restr	0.003	885

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 (%)
2.1956-2.2505	0.3615	90	0.3396	1308	X-RAY DIFFRACTION	37
2.2505-2.3113	0.3698	84	0.3282	1505	X-RAY DIFFRACTION	42
2.3113-2.3793	0.4307	81	0.3242	1623	X-RAY DIFFRACTION	45
2.3793-2.4561	0.418	94	0.3303	1750	X-RAY DIFFRACTION	49
2.4561-2.5439	0.3463	109	0.3386	1942	X-RAY DIFFRACTION	53
2.5439-2.6458	0.3486	127	0.3283	2132	X-RAY DIFFRACTION	59
2.6458-2.7662	0.3574	131	0.3258	2393	X-RAY DIFFRACTION	66
2.7662-2.912	0.3155	135	0.3134	2667	X-RAY DIFFRACTION	73
2.912-3.0945	0.3086	148	0.3178	2950	X-RAY DIFFRACTION	80
3.0945-3.3334	0.3148	169	0.2752	3258	X-RAY DIFFRACTION	89
3.3334-3.6688	0.2577	173	0.2465	3614	X-RAY DIFFRACTION	98
3.6688-4.1996	0.245	188	0.2078	3711	X-RAY DIFFRACTION	100
4.1996-5.2905	0.2043	222	0.1757	3740	X-RAY DIFFRACTION	100
5.2905-60.7955	0.2156	221	0.2156	3877	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	0.2158	0.1399	0.5259	0.4208	0.2396	1.4653	-0.0936	0.2717	-0.0523	-0.1743	0.1272	-0.1271	-0.2749	0.4184	-0.2756	0.3604	-0.1494	0.0345	0.4663	-0.1962	0.2759	-7.7207	-18.9244	-48.7394
2	0.7521	0.1337	0.4383	0.0954	0.1393	0.7326	-0.1657	0.2542	-0.0602	-0.1657	0.0417	-0.0984	-0.4423	0.4068	0.0453	0.3468	-0.1632	0.0432	0.5041	-0.1748	0.3392	-6.1446	-18.2544	-42.4558
3	0.5512	0.197	-0.0507	0.2994	0.0988	1.0526	-0.1006	-0.0439	0.0147	-0.0812	-0.0618	0.0583	-0.53	0.1611	0.072	0.4433	-0.1514	0.045	0.463	-0.1363	0.2413	-8.9047	-12.1169	-15.7128
4	4.8927	0.0821	0.4255	0.2596	0.2932	1.19	-0.1692	0.0811	0.4447	-0.193	0.0848	-0.0219	-0.526	0.0691	0.0467	0.9036	-0.1365	-0.0711	0.5711	-0.2338	0.4743	-18.1818	-4.1468	-39.8522
5	0.3413	-0.148	0.043	1.1771	-0.2332	0.0467	-0.0978	0.0238	0.0509	-0.0555	0.001	0.0177	-0.4144	-0.0012	0.1022	0.395	-0.0587	-0.0157	0.3377	-0.2178	0.3225	-22.7048	-15.6995	-48.6509
6	0.3205	-0.2157	0.581	2.7297	-0.5131	1.1414	-0.0604	-0.3984	-0.2321	0.5181	-0.1006	0.2323	0.2922	0.0349	0.1822	0.499	-0.1758	0.2245	0.7865	-0.2436	0.5647	-35.6068	-36.2533	-16.434
7	0.6399	0.1353	0.1883	0.8614	1.155	1.5473	-0.0187	0.0424	-0.1621	0.1199	-0.1816	0.2341	0.2148	-0.2592	0.2163	0.2147	-0.0542	0.0835	0.4867	-0.2497	0.4243	-29.3788	-31.6078	-27.1371
8	0.6882	-0.199	-1.0363	0.5066	0.8571	3.5007	-0.1782	-0.0577	-0.2405	0.0879	-0.1478	0.225	0.378	-0.1449	0.3487	0.2349	-0.0173	0.0871	0.5243	-0.2458	0.4811	-20.9752	-35.2662	-34.5252
9	1.4657	-0.2059	-0.2211	0.158	0.4081	1.5882	-0.0937	-0.0035	-0.301	0.1796	-0.048	0.1151	0.3797	-0.1835	0.1514	0.4528	-0.2236	0.1818	0.7754	-0.325	0.6487	-42.4813	-36.9301	-22.3288
10	0.5638	-0.1442	-0.1577	0.4322	0.3169	1.6592	-0.0153	0.0232	-0.1252	0.033	-0.1701	0.1776	0.2843	-0.1521	0.2354	0.282	-0.0484	0.0877	0.5555	-0.3262	0.5729	-38.5565	-37.4137	-37.8634
11	0.007	-0.0098	-0.0115	0.3049	0.2176	0.3719	-0.0067	0.0237	-0.0299	0.0672	-0.0179	0.0421	0.0628	-0.0247	-0.0461	0.2425	0.0247	-0.0125	0.5136	-0.3466	0.4766	-31.4977	-32.9576	-58.428
12	0.09	-0.0597	0.0109	0.3331	0.225	0.5044	-0.0254	0.0311	-0.0383	0.0686	-0.0276	0.0251	0.1091	-0.0726	-0.0558	0.2368	0.0014	-0.0026	0.5359	-0.3619	0.5375	-36.2759	-37.9154	-59.4769
13	2.0291	0.0278	-1.8904	2.8374	0.5298	3.073	0.1097	0.1869	-0.0189	0.1534	-0.1258	0.3495	-0.3008	-0.4402	0.011	0.5329	0.179	0.0226	0.6392	-0.3147	0.5849	-42.3648	-19.5011	-32.3782
14	0.4115	-0.1642	-0.1875	0.4502	0.4015	0.8619	0.0173	-0.0824	-0.0114	0.0521	-0.0382	0.0941	-0.1869	-0.143	-0.0442	0.2604	0.0363	0.0427	0.4246	-0.2237	0.3333	-29.9574	-19.1239	-24.0666

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 251 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 252 through 273 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 274 through 324 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -1 through 24 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 81 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 82 through 114 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 115 through 141 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 142 through 198 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 199 through 256 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 257 through 278 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 279 through 323 )

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