PDB-6n7f: 1.90 Angstrom Resolution Crystal Structure of Glutathione Reducta...

ID or keywords:

Entry

Database: PDB / ID: 6n7f

Title

1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD.

Components

Putative glutathione reductase (GR)

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD

Function / homology

Function and homology information

glutathione-disulfide reductase / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding / cellular response to oxidative stress / cytosol
Similarity search - Function

Biological species

Streptococcus pyogenes serotype M1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Minasov, G. / Shuvalova, L. / Shabalin, I.G. / Grabowski, M. / Olphie, A. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.90 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus pyogenes in Complex with FAD.
Authors: Minasov, G. / Shuvalova, L. / Shabalin, I.G. / Grabowski, M. / Olphie, A. / Cardona-Correa, A. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 27, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	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	6n7f.cif.gz	750 KB	Display	PDBx/mmCIF format
PDB format	pdb6n7f.ent.gz	620.5 KB	Display	PDB format
PDBx/mmJSON format	6n7f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6n7f_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	6n7f_full_validation.pdf.gz	2 MB	Display
Data in XML	6n7f_validation.xml.gz	81.4 KB	Display
Data in CIF	6n7f_validation.cif.gz	123.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n7/6n7f ftp://data.pdbj.org/pub/pdb/validation_reports/n7/6n7f	HTTPS FTP

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Related structure data

Related structure data	5v36S S: Starting model for refinement
Similar structure data	3sqp-d 6i4t-d 6oez-d 1geu-d 6oex-d 1ojt-1 3lad-d 6hg8-d 3djg-1 1gsn-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP07597

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (8) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Putative glutathione reductase (GR)

B: Putative glutathione reductase (GR)

C: Putative glutathione reductase (GR)

D: Putative glutathione reductase (GR)

hetero molecules

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

1

A: Putative glutathione reductase (GR)

B: Putative glutathione reductase (GR)

hetero molecules

defined by author&software
Evidence: homology, 5V36
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative glutathione reductase (GR)

D: Putative glutathione reductase (GR)

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.400, 86.650, 86.670
Angle α, β, γ (deg.)	67.13, 74.15, 74.11
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Putative glutathione reductase (GR) Mass: 49246.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Gene: gor, SPy_0813 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9A0E2, glutathione-disulfide reductase

#1: Protein

Putative glutathione reductase (GR)

Mass: 49246.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes serotype M1 (bacteria)
Gene: gor, SPy_0813 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9A0E2, glutathione-disulfide reductase

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Non-polymers , 7 types, 1736 molecules

#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-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₄O₆
#4: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#5: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO₃
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1708 / 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: 2.54 Å³/Da / Density % sol: 51.61 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 9.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD; Screen: Classics II (F10), 0.2M Sodium chloride, 0.1M Bis-Tris pH=5.5, 25% (w/v) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2017 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 148744 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / B_iso Wilson estimate: 23 Å² / R_merge(I) obs: 0.069 / R_pim(I) all: 0.058 / R_rim(I) all: 0.091 / R_sym value: 0.069 / Χ²: 1.014 / Net I/σ(I): 12
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.517 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7256 / CC_1/2: 0.657 / R_pim(I) all: 0.439 / R_rim(I) all: 0.681 / R_sym value: 0.517 / Χ²: 0.992 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5V36

5v36

Resolution: 1.9→29.47 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.945 / SU B: 8.089 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21042	7232	4.9 %	RANDOM
R_work	0.16896	-	-	-
obs	0.171	141509	97.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.814 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.41 Å²	-0.32 Å²	-0.33 Å²
2-	-	-0.2 Å²	-0.05 Å²
3-	-	-	-0.38 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→29.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13806	0	320	1708	15834

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	14987
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	13876
X-RAY DIFFRACTION	r_angle_refined_deg	1.41	1.643	20415
X-RAY DIFFRACTION	r_angle_other_deg	0.377	1.579	32182
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.506	5	1916
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.273	22.795	730
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.817	15	2474
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.818	15	77
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	1952
X-RAY DIFFRACTION	r_gen_planes_refined	0.055	0.02	17167
X-RAY DIFFRACTION	r_gen_planes_other	0.051	0.02	3124
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.975	1.562	7472
X-RAY DIFFRACTION	r_mcbond_other	0.974	1.562	7471
X-RAY DIFFRACTION	r_mcangle_it	1.537	2.34	9425
X-RAY DIFFRACTION	r_mcangle_other	1.537	2.34	9426
X-RAY DIFFRACTION	r_scbond_it	1.649	1.854	7515
X-RAY DIFFRACTION	r_scbond_other	1.649	1.854	7516
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.592	2.69	10982
X-RAY DIFFRACTION	r_long_range_B_refined	5.176	20.169	17210
X-RAY DIFFRACTION	r_long_range_B_other	4.938	19.431	16810
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	520	-
R_work	0.26	10046	-
obs	-	-	93.75 %

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	1.7127	-0.0092	-0.5636	2.0905	0.0932	1.2634	0.0949	-0.1587	-0.0633	0.2133	0.0215	0.1332	0.0418	-0.0461	-0.1164	0.1732	-0.016	0.0124	0.0256	0.0216	0.0321	-29.8274	-48.0742	-22.9646
2	2.4837	0.4867	0.2456	0.1327	0.0706	0.5386	-0.0214	0.0676	-0.095	0.0189	0.0779	-0.0323	0.0598	0.0841	-0.0564	0.2423	0.0119	-0.027	0.1117	-0.0213	0.0911	3.045	-48.7694	-25.6929
3	1.9683	0.2624	-0.5468	0.6131	-0.0149	0.5156	-0.0174	-0.0124	-0.073	0.0616	0.046	0.018	0.0883	0.033	-0.0286	0.1685	-0.0035	-0.0247	0.021	0.0021	0.0136	-14.5252	-49.2574	-35.2242
4	1.1666	-0.499	-0.3261	2.9935	1.5453	1.8678	0.113	0.2744	0.0227	-0.2819	-0.1583	-0.0844	-0.1303	-0.1285	0.0453	0.1213	-0.0131	0.0081	0.0881	0.0049	0.0099	1.8997	-39.9349	-48.5415
5	1.3159	0.0378	0.5862	0.7787	0.0472	0.3354	-0.0481	0.0002	0.1396	0.0767	0.0132	0.1096	-0.0283	0.0282	0.0349	0.1719	-0.0147	0.012	0.0223	0.0007	0.052	-23.3582	-35.9237	-32.126
6	0.5607	-0.3348	0.0763	0.4199	-0.0362	1.329	-0.0888	0.0406	0.1503	0.0128	0.0346	-0.0435	-0.1988	0.0435	0.0542	0.2233	-0.0427	-0.0416	0.0217	0.0245	0.0509	0.2284	-19.5895	-27.1322
7	0.6558	0.4408	0.4276	1.5643	0.6923	0.5014	-0.0745	0.0803	0.1042	-0.1585	0.0544	-0.0541	-0.1588	0.1432	0.0201	0.273	-0.066	-0.0109	0.1043	-0.0025	0.0371	18.985	-18.9532	-14.9658
8	0.4563	0.183	0.425	4.0254	1.1063	0.8065	-0.0483	0.1336	-0.0342	-0.3319	0.1124	-0.2836	-0.1927	0.238	-0.0641	0.1952	-0.0479	0.02	0.1165	-0.0061	0.0297	25.4817	-24.8802	-19.4371
9	0.7079	0.079	0.1514	0.4943	-0.1225	0.8881	-0.0461	-0.0247	0.041	0.0039	0.0382	-0.0094	-0.0066	0.1807	0.0079	0.1717	0.0012	-0.0255	0.0864	-0.0247	0.019	18.4999	-26.0804	-0.8089
10	1.0096	0.601	0.7631	0.7127	0.5819	2.0188	0.0443	0.1284	-0.2186	0.0322	0.0936	-0.0933	0.348	0.3111	-0.1379	0.198	0.0725	-0.0211	0.1047	-0.0261	0.0532	22.6324	-38.5194	8.2744
11	1.3989	0.7523	0.2951	1.8943	0.3208	1.1865	-0.069	-0.1045	0.2768	0.0621	-0.0018	0.1461	-0.2482	0.0524	0.0708	0.2612	-0.0365	-0.051	0.0208	-0.0173	0.0637	11.4074	-8.2487	-4.0041
12	0.9539	-0.4804	0.2874	0.8898	0.1684	1.341	-0.0361	-0.0572	0.0015	0.0352	-0.0265	0.0738	-0.0416	-0.0808	0.0626	0.1546	-0.0194	-0.013	0.0157	-0.0041	0.0109	-7.4875	-30.5686	-9.8002
13	2.814	1.0122	-0.4947	0.6376	-0.2661	3.0869	-0.1823	0.2017	-0.0015	-0.2614	0.0532	0.1627	-0.3175	-0.0839	0.1291	0.3671	-0.0564	-0.0978	0.1061	-0.0041	0.1341	-46.9283	-14.4255	-80.9132
14	0.6404	0.6965	0.5087	1.4616	1.2788	1.5765	0.0027	0.0111	0.0941	-0.1534	-0.0146	0.161	-0.1012	-0.0866	0.0119	0.2393	-0.0069	-0.0302	0.0121	0.0208	0.1297	-46.1181	-1.4613	-56.8128
15	0.7821	0.1392	0.0491	0.6868	-0.1975	0.787	-0.0574	0.0455	-0.01	-0.0068	0.0618	0.1537	0.0244	0.0047	-0.0044	0.1995	-0.0234	0.0049	0.0098	0.0094	0.147	-43.3057	-18.7506	-54.2059
16	2.1866	1.5131	0.6615	2.3013	-0.258	0.6197	0.0734	-0.1922	0.3145	0.3506	-0.0602	0.3646	-0.1423	-0.0965	-0.0132	0.2243	0.0055	0.0828	0.0308	-0.0181	0.1448	-47.6122	-23.1308	-38.7282
17	1.0511	0.3832	0.6016	0.6667	0.0439	0.9048	-0.0735	0.1677	-0.1741	-0.2066	0.0953	0.0014	0.0878	0.0689	-0.0219	0.2678	-0.0565	-0.0029	0.0345	-0.0265	0.0668	-34.6174	-21.2694	-69.7574
18	0.6439	0.172	-0.4158	1.2171	0.1258	0.9147	-0.022	0.0052	-0.0087	-0.018	0.0405	-0.1148	0.0421	0.0493	-0.0185	0.1764	-0.0122	-0.0121	0.0075	0.0065	0.065	-16.8087	-7.6614	-52.9024
19	1.0669	0.0605	-0.1653	1.5924	0.6615	2.3047	0.103	-0.0617	-0.2064	0.128	-0.0581	0.0394	0.218	0.1456	-0.045	0.2041	0.0117	-0.0257	0.0414	0.0194	0.059	5.0173	9.5468	-41.0641
20	3.0683	0.2958	0.5	0.5752	-0.0801	0.1293	-0.0359	-0.0501	0.0865	0.0679	-0.0077	0.0937	-0.0074	0.0013	0.0436	0.2066	-0.0124	0.029	0.0575	-0.0026	0.1444	-27.852	12.2964	-41.3028
21	2.166	-0.2935	0.4249	0.3752	0.0255	0.5203	-0.0211	-0.0767	0.0452	0.0863	-0.0068	0.0518	0.0228	0.0351	0.0279	0.1782	-0.0198	0.0017	0.0163	0.0103	0.0551	-9.5992	21.2994	-43.9161
22	1.0388	-0.3937	-0.3083	3.0713	1.5817	2.3041	0.0896	0.1202	0.2377	-0.158	-0.0634	-0.1011	-0.1793	-0.1398	-0.0262	0.0926	0.0106	-0.0227	0.0215	0.032	0.0988	-26.9337	30.7645	-57.1687
23	1.1019	0.5495	-0.0559	0.4566	0.1683	0.7961	-0.0316	0.1057	-0.0583	-0.0077	0.063	-0.002	0.0843	0.0958	-0.0314	0.1615	0.0091	-0.0192	0.0318	-0.0015	0.0358	-1.4129	14.032	-55.5784
24	0.5231	0.0198	-0.3756	1.0299	-0.223	0.4893	-0.0771	0.1239	-0.0023	-0.1625	0.0475	0.0564	0.0943	-0.0562	0.0297	0.2186	-0.0465	-0.0282	0.0438	0.0143	0.0229	-25.0177	3.7751	-69.2604

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 37
2	X-RAY DIFFRACTION	2	A	38 - 100
3	X-RAY DIFFRACTION	3	A	101 - 193
4	X-RAY DIFFRACTION	4	A	194 - 261
5	X-RAY DIFFRACTION	5	A	262 - 351
6	X-RAY DIFFRACTION	6	A	352 - 450
7	X-RAY DIFFRACTION	7	B	1 - 72
8	X-RAY DIFFRACTION	8	B	73 - 114
9	X-RAY DIFFRACTION	9	B	115 - 220
10	X-RAY DIFFRACTION	10	B	221 - 263
11	X-RAY DIFFRACTION	11	B	264 - 347
12	X-RAY DIFFRACTION	12	B	348 - 450
13	X-RAY DIFFRACTION	13	C	1 - 37
14	X-RAY DIFFRACTION	14	C	38 - 114
15	X-RAY DIFFRACTION	15	C	115 - 220
16	X-RAY DIFFRACTION	16	C	221 - 262
17	X-RAY DIFFRACTION	17	C	263 - 360
18	X-RAY DIFFRACTION	18	C	361 - 450
19	X-RAY DIFFRACTION	19	D	0 - 37
20	X-RAY DIFFRACTION	20	D	38 - 100
21	X-RAY DIFFRACTION	21	D	101 - 191
22	X-RAY DIFFRACTION	22	D	192 - 261
23	X-RAY DIFFRACTION	23	D	262 - 351
24	X-RAY DIFFRACTION	24	D	352 - 450

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