PDB-5v36: 1.88 Angstrom Resolution Crystal Structure of Glutathione Reducta...

ID or keywords:

Entry

Database: PDB / ID: 5v36

Title

1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD

Components

Glutathione reductase

Keywords

HYDROLASE / 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 mutans serotype c (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 Å

Authors

Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...

History

Deposition	Mar 6, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Feb 11, 2026	Group: Database references / Structure summary Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5v36.cif.gz	403.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5v36.ent.gz	330 KB	Display	PDB format
PDBx/mmJSON format	5v36.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/v3/5v36 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/5v36	HTTPS FTP

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Related structure data

Related structure data	5tr3C 5tv2C 5ty0C 5u1oSC 5u2gC 5u47C 5ue1C 5umeC 5us8C 5uswC 5usxC 5utxC 5uu6C 5uwyC 5ux9C 5vdnC 5vfbC 5vh6C 5wi5C 5wp0C 6aonC 6aooC 6awaC 6aziC 6b4oC 6b5fC 6b8dC 6balC 6bk7C 6blbC 6bq9C 6bz0C 6c8qC 6cmzC 6cn1C 6czpC 6e5yC 6muqC 6n0iC 6n7fC 6nfpC 6nkjC 6po4C 6pu9C 6puaC 6pxaC 6w2zC 9bznC 9bzqC 9bzrC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5u1o-1 4dna-d 6du7-4 6b4o-1 6du7-2 1grg-1 2wov-1 5grt-1 1gxf-d 5u1o-2 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-IDP07311

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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) #82 - Oct 2006 Cytochrome p450 similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Glutathione reductase

B: Glutathione reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

2

A: Glutathione reductase

B: Glutathione reductase

hetero molecules

A: Glutathione reductase

B: Glutathione reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	126.333, 126.333, 247.876
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein

Glutathione reductase

Mass: 49307.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: gshR, SMU_838 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic
References: UniProt: Q8DUR5, adenosylhomocysteinase, glutathione-disulfide reductase

#8: Sugar

ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

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Non-polymers , 7 types, 1082 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.8 Å³/Da / Density % sol: 56.1 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 8.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1.mM FAD; Screen: Classics II (A5), 2M Ammonium sulfate, 0.1 HEPES (pH 7.5); Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2017 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.88→30 Å / Num. obs: 95700 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / B_iso Wilson estimate: 27.8 Å² / R_merge(I) obs: 0.076 / R_pim(I) all: 0.02 / R_sym value: 0.076 / Χ²: 1.003 / Net I/σ(I): 35.2
Reflection shell	Resolution: 1.88→1.91 Å / Redundancy: 14 % / R_merge(I) obs: 0.775 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4685 / CC_1/2: 0.888 / R_pim(I) all: 0.21 / R_sym value: 0.775 / Χ²: 0.997 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5U1O

5u1o

Resolution: 1.88→29.81 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.967 / SU B: 4.126 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17048	4741	5 %	RANDOM
R_work	0.14286	-	-	-
obs	0.14424	90417	99.93 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.111 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.32 Å²	-0.16 Å²	0 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	1.03 Å²

Refinement step

Cycle: 1 / Resolution: 1.88→29.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6914	0	329	1034	8277

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	7886
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7037
X-RAY DIFFRACTION	r_angle_refined_deg	1.377	1.983	10782
X-RAY DIFFRACTION	r_angle_other_deg	0.849	3.001	16353
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.865	5	1010
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.838	24.435	345
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.103	15	1263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.813	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1198
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	8947
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	1604
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	0.94	1.946	3890
X-RAY DIFFRACTION	r_mcbond_other	0.939	1.945	3889
X-RAY DIFFRACTION	r_mcangle_it	1.402	2.913	4950
X-RAY DIFFRACTION	r_mcangle_other	1.402	2.914	4951
X-RAY DIFFRACTION	r_scbond_it	1.838	2.362	3996
X-RAY DIFFRACTION	r_scbond_other	1.837	2.362	3996
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.756	3.446	5833
X-RAY DIFFRACTION	r_long_range_B_refined	5.924	25.807	9291
X-RAY DIFFRACTION	r_long_range_B_other	5.653	24.678	9006
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.88→1.929 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.21	338	-
R_work	0.184	6531	-
obs	-	-	99.74 %

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	1.7616	0.3063	0.2882	3.1904	0.3726	1.7112	-0.0551	0.213	0.0252	-0.412	-0.0073	-0.0904	0.0554	-0.0011	0.0623	0.1141	-0.0398	-0.0019	0.0961	0.0357	0.0214	15.6827	82.1498	-6.387
2	1.8825	-0.2206	0.8651	0.1514	0.0355	0.7472	-0.0739	0.0104	0.2031	-0.0347	0.0213	-0.0542	-0.1329	-0.0164	0.0526	0.0895	-0.0339	0.0037	0.0721	0.0481	0.1035	40.0923	96.14	11.0238
3	0.7164	0.6175	0.5624	1.2125	0.4414	1.2151	-0.0948	0.0894	0.049	-0.2069	0.0811	0.0546	-0.1131	-0.0874	0.0137	0.0629	-0.0094	-0.0157	0.0817	0.0534	0.0509	15.0242	91.6588	0.6294
4	0.9558	-0.4827	0.1554	0.9255	-0.3011	1.323	0.012	-0.0432	0.1317	0.0351	0.0336	0.0463	-0.2281	-0.0495	-0.0455	0.0645	-0.0227	0.0087	0.0476	0.0104	0.0457	26.8359	101.0937	26.4315
5	0.3487	0.1589	0.1319	0.3088	0.002	0.5583	0.0331	-0.0554	0.0043	-0.0229	-0.0391	0.0513	0.0288	-0.0984	0.0061	0.0405	-0.0235	-0.0163	0.0705	0.0331	0.0456	16.5121	83.1628	13.2792
6	3.1869	2.1729	-0.8146	2.427	-0.1007	0.4984	0.0731	-0.1977	-0.0031	0.1388	-0.0595	-0.0029	0.0191	0.0113	-0.0136	0.0959	-0.0384	-0.0326	0.135	0.0559	0.0519	34.729	77.1085	33.9041
7	0.7396	0.0498	-0.0296	1.079	0.281	0.5262	0.0012	-0.0954	-0.0679	0.0093	-0.0182	-0.0066	0.0494	-0.0226	0.017	0.0547	-0.034	-0.0204	0.082	0.0636	0.0522	37.1495	71.9827	25.7651
8	3.069	0.4066	-0.3863	3.0913	-0.8256	1.7531	-0.0162	-0.2771	0.0854	0.3234	-0.0304	0.0048	-0.0596	0.0622	0.0466	0.0762	0.0105	0.0083	0.0493	0.007	0.0127	59.9056	60.9661	44.5634
9	0.4599	-0.1789	0.038	0.6196	-0.1822	0.2856	-0.0184	-0.0308	0.0626	0.056	0.0061	-0.0376	-0.0041	0.0804	0.0123	0.0364	-0.0139	-0.0001	0.0505	0.0083	0.0309	62.4673	75.9986	30.4177
10	1.1873	0.0869	0.3183	0.6107	0.2242	0.4576	0.0132	0.0217	0.035	-0.0445	0.0269	-0.0142	0.046	0.0048	-0.04	0.0859	-0.0388	0.0048	0.0551	0.0317	0.0459	62.6707	77.0186	10.0167
11	2.1397	-0.1875	0.0037	1.4563	0.008	1.1234	0.0005	0.0344	0.0794	-0.216	-0.0056	-0.0958	0.0955	0.1715	0.005	0.0821	-0.0152	0.0234	0.0732	0.0167	0.0297	75.5707	77.0195	9.2802
12	1.7191	0.2403	0.0359	1.2567	-0.2309	1.1466	-0.0253	0.0491	-0.0742	-0.0956	0.0223	0.0522	0.1463	-0.0131	0.0031	0.0748	0.0083	0.0096	0.039	0.0317	0.0361	57.6502	54.8311	31.0968
13	0.746	0.3431	-0.3789	2.4187	0.051	0.292	-0.0085	0.03	-0.0543	-0.194	-0.0095	-0.041	0.0045	0.0039	0.018	0.0872	-0.0372	-0.0213	0.0641	0.0429	0.0512	44.6142	69.7342	7.574
14	0.7541	0.2927	-0.0494	1.4212	0.1786	0.5522	0.0212	-0.0097	-0.0437	-0.1154	-0.0249	0.0794	0.0296	-0.0433	0.0036	0.0724	-0.0227	-0.024	0.0585	0.0508	0.0578	35.5571	71.1476	13.4778

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 - 98
3	X-RAY DIFFRACTION	3	A	99 - 161
4	X-RAY DIFFRACTION	4	A	162 - 249
5	X-RAY DIFFRACTION	5	A	250 - 360
6	X-RAY DIFFRACTION	6	A	361 - 401
7	X-RAY DIFFRACTION	7	A	402 - 450
8	X-RAY DIFFRACTION	8	B	0 - 37
9	X-RAY DIFFRACTION	9	B	38 - 161
10	X-RAY DIFFRACTION	10	B	162 - 220
11	X-RAY DIFFRACTION	11	B	221 - 263
12	X-RAY DIFFRACTION	12	B	264 - 337
13	X-RAY DIFFRACTION	13	B	338 - 410
14	X-RAY DIFFRACTION	14	B	411 - 450

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