PDB-5u1o: 2.3 Angstrom Resolution Crystal Structure of Glutathione Reductas...

ID or keywords:

Entry

Database: PDB / ID: 5u1o

Title

2.3 Angstrom Resolution Crystal Structure of Glutathione Reductase from Vibrio parahaemolyticus in Complex with FAD.

Components

Glutathione reductase

Keywords

LIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD / Lipid-Binding Protein

Function / homology

Function and homology information

glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Vibrio parahaemolyticus serotype O3:K6

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.31 Å

Authors

Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / 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	Nov 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_keywords Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords
Revision 1.2	Oct 30, 2024	Group: Structure summary Category: pdbx_entry_details / pdbx_modification_feature / struct_keywords Item: _struct_keywords.text
Revision 1.3	Feb 11, 2026	Group: Database references / Category: citation / citation_author 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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Download

PDBx/mmCIF format	5u1o.cif.gz	701 KB	Display	PDBx/mmCIF format
PDB format	pdb5u1o.ent.gz	581.1 KB	Display	PDB format
PDBx/mmJSON format	5u1o.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/u1/5u1o ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u1o	HTTPS FTP

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Related structure data

Related structure data	5tr3C 5tv2C 5ty0C 5u2gC 5u47C 5ue1C 5umeC 5us8C 5uswC 5usxC 5utxC 5uu6C 5uwyC 5ux9C 5v36C 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 1gesS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6b4o-1 5v36-d 4dna-d 6du7-4 6du7-2 5x1y-2 2wov-1 5grt-1 1xan-1 1zmd-3 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-IDP07224

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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)

Deposited unit

A: Glutathione reductase

B: Glutathione reductase

C: Glutathione reductase

D: Glutathione reductase

hetero molecules

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

1

A: Glutathione reductase

B: Glutathione reductase

hetero molecules

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

2

C: Glutathione reductase

D: Glutathione reductase

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)	58.528, 174.289, 206.094
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Glutathione reductase Mass: 49605.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) Strain: RIMD 2210633 / Gene: VP0068 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q87TK1
#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.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H₂O
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: 2.65 Å³/Da / Density % sol: 53.56 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 16.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD, Screen: PACT (C10), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.0), 20% (w/v) PEG 6000

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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: Nov 15, 2016 / 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: 2.3→30 Å / Num. obs: 86905 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / B_iso Wilson estimate: 45 Å² / R_merge(I) obs: 0.104 / R_sym value: 0.104 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.627 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4326 / CC_1/2: 0.919 / % possible all: 93.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GES

1ges

Resolution: 2.31→29.95 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.929 / SU B: 16.848 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24854	4409	5.1 %	RANDOM
R_work	0.20202	-	-	-
obs	0.20436	82358	92.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 45.556 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.42 Å²	0 Å²	0 Å²
2-	-	-0.77 Å²	0 Å²
3-	-	-	-5.65 Å²

Refinement step

Cycle: 1 / Resolution: 2.31→29.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13692	0	233	806	14731

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	14293
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	13434
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.967	19427
X-RAY DIFFRACTION	r_angle_other_deg	0.888	3	30966
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.522	5	1812
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.009	25.024	613
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.801	15	2324
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.606	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	2169
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	16262
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	3132
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	1.221	2.822	7239
X-RAY DIFFRACTION	r_mcbond_other	1.221	2.821	7238
X-RAY DIFFRACTION	r_mcangle_it	1.98	4.23	9054
X-RAY DIFFRACTION	r_mcangle_other	1.98	4.23	9055
X-RAY DIFFRACTION	r_scbond_it	1.559	3.079	7054
X-RAY DIFFRACTION	r_scbond_other	1.538	3.075	7039
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.527	4.535	10350
X-RAY DIFFRACTION	r_long_range_B_refined	4.654	33.914	16083
X-RAY DIFFRACTION	r_long_range_B_other	4.573	33.651	15931
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.306→2.365 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	323	-
R_work	0.325	5772	-
obs	-	-	89.08 %

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	3.1484	0.4574	0.3397	1.6877	1.7575	1.8695	-0.0299	-0.0258	-0.0113	0.0744	0.0978	-0.1047	0.1309	0.1968	-0.0679	0.1	0.1411	0.0075	0.3734	0.0092	0.3603	31.6749	10.5967	29.2832
2	0.9593	-1.4219	-0.1441	3.0774	-0.7971	1.267	0.0009	0.0262	-0.0133	-0.1354	-0.0416	-0.037	0.0292	0.0284	0.0407	0.0871	0.0077	-0.003	0.161	-0.0208	0.1483	12.3992	26.4189	9.9396
3	2.1336	-0.0078	0.6922	1.137	-0.304	1.593	-0.015	0.0446	-0.1684	-0.1982	0.0021	-0.3243	0.337	0.344	0.013	0.1042	0.0903	0.0528	0.1515	-0.0318	0.2195	24.3365	4.0315	23.308
4	0.3083	0.1323	-0.4109	2.1471	0.9537	3.0913	0.0119	0.0567	-0.073	-0.1675	-0.079	0.2177	0.0264	-0.459	0.0671	0.0285	0.0076	-0.0521	0.1952	-0.0334	0.1879	-3.3272	13.8146	13.4653
5	1.21	-0.3219	0.6855	0.8513	0.1681	1.8177	0.0074	-0.0562	-0.0595	-0.0069	0.0778	-0.0776	0.2024	0.053	-0.0852	0.035	0.0237	-0.0065	0.0937	0.0066	0.1859	14.7591	10.0383	31.4313
6	0.0031	-0.0298	0.0208	1.1127	-0.643	2.6629	0.006	0.0021	0.0229	-0.0809	0.046	0.1291	-0.0104	-0.1897	-0.052	0.0126	0.0304	0.0145	0.2674	0.0068	0.3272	-1.7368	32.5157	34.0036
7	0.0481	-0.0824	0.0145	0.9167	0.163	0.4399	0.0122	-0.0012	-0.0072	-0.0952	0.0075	0.1759	-0.1263	-0.0497	-0.0196	0.0503	0.0566	0.0025	0.2329	0.007	0.2197	-4.098	52.4009	25.2547
8	4.254	-0.6048	-5.8868	0.1434	0.814	8.4392	-0.0607	0.1984	-0.1816	0.0017	-0.1036	0.0851	0.2584	-0.2849	0.1642	0.1191	0.0076	-0.0167	0.1672	-0.0215	0.1375	-4.9266	49.7697	11.4483
9	1.7226	0.6594	-0.6578	5.3731	1.3452	2.1546	-0.0617	0.1341	0.1327	0.0824	0.0415	0.3901	-0.0862	-0.3014	0.0203	0.038	0.0576	0.0337	0.1377	0.0408	0.1578	-13.8778	65.8454	36.4147
10	1.2368	-0.4736	0.016	2.2997	-0.5741	1.9969	0.0826	0.1351	0.1108	-0.1272	-0.0696	-0.0734	-0.2761	0.1687	-0.0131	0.0921	0.0255	0.0539	0.122	0.0101	0.1395	14.5848	58.3389	16.0746
11	0.594	-0.214	-0.2751	1.077	0.0067	1.2734	0.0174	-0.0172	0.0596	-0.0208	0.0197	0.0166	-0.1254	0.0131	-0.0372	0.0245	0.0309	0.0037	0.0915	0.0036	0.1794	5.969	62.6337	31.6113
12	0.4595	0.1838	0.7764	1.1011	0.8289	1.8462	0.0244	0.0717	-0.0548	-0.132	0.0329	-0.0332	-0.0581	0.1531	-0.0573	0.0264	0.0158	0.0196	0.255	-0.0021	0.3099	19.3211	38.1039	31.8242
13	2.4724	-1.9011	-0.2376	3.4348	2.5456	3.028	-0.0305	-0.111	-0.0017	0.1053	0.1582	-0.2364	0.0453	0.2386	-0.1277	0.0329	-0.0772	-0.0212	0.2374	0.0008	0.285	38.7525	54.7572	67.8285
14	0.7703	0.9855	-0.0081	2.1458	-0.697	1.003	0.1502	-0.1143	0.0963	0.4621	-0.0767	0.0137	-0.1413	0.0312	-0.0735	0.1467	-0.0372	-0.0216	0.2048	0.0012	0.1805	21.7973	39.7687	91.8809
15	1.4714	-0.4262	-0.975	1.6592	-0.1145	1.8016	0.0587	-0.0806	0.1276	0.3396	-0.0574	-0.3628	-0.1886	0.3076	-0.0013	0.1044	-0.076	-0.0627	0.1669	-0.0263	0.2378	33.0416	60.1254	76.6497
16	1.5175	0.0845	0.2821	2.7372	0.7099	2.2564	0.1251	-0.2677	0.1426	0.4892	-0.0318	0.182	-0.2611	-0.3474	-0.0933	0.2139	-0.0157	0.0991	0.157	-0.0289	0.1041	7.5357	54.8599	92.2039
17	0.3922	0.0895	0.1918	0.6709	0.049	0.3267	0.0316	0.0101	0.0555	0.0792	0.0096	-0.0365	-0.1128	-0.0239	-0.0413	0.0904	-0.0192	0.0269	0.1617	0.0128	0.2164	16.5485	52.353	68.1461
18	0.3079	-0.1097	0.8562	1.3509	-0.1702	2.3971	0.025	-0.0501	-0.0224	0.2514	0.0065	0.1594	0.0926	-0.1598	-0.0316	0.055	-0.0266	0.0327	0.2407	0.0312	0.3067	4.4	33.9256	70.7976
19	1.3763	-1.1761	1.079	4.1849	-0.4863	2.5067	0.0658	-0.1159	0.0072	0.3322	0.096	0.5032	0.2356	-0.3641	-0.1618	0.0618	-0.0197	0.0543	0.3799	0.1505	0.3442	-12.4088	9.3314	69.5067
20	0.5303	0.2554	-0.467	1.5117	0.2238	0.6027	0.0126	0.0336	-0.0653	0.1622	-0.0459	0.024	-0.0428	-0.0774	0.0332	0.1846	-0.0247	0.0136	0.2305	0.0498	0.1732	8.7124	20.9751	91.5235
21	2.637	-1.2207	-0.4284	7.6426	1.7592	3.2867	-0.1973	-0.4482	-0.1554	0.2926	0.3245	0.6601	0.0806	-0.2696	-0.1272	0.0411	-0.0002	0.0132	0.1907	0.0928	0.1297	-13.264	5.7824	72.7903
22	0.461	0.3509	-0.0923	0.7944	-0.2319	1.1015	0.0589	-0.025	-0.0448	0.1619	-0.0041	0.0347	0.1482	0.0704	-0.0547	0.0826	-0.0279	-0.0098	0.1495	0.0466	0.1987	13.2239	6.2035	81.6325
23	0.9055	-0.0962	0.2867	1.1225	-0.7851	1.4931	-0.0136	-0.0439	-0.0576	0.0273	0.0687	0.1155	0.0331	-0.1161	-0.0551	0.0065	-0.0147	0.0039	0.0865	0.0177	0.1768	9.0011	4.908	72.3774
24	0.0278	-0.0613	-0.1861	0.8202	-0.0255	1.8571	-0.001	-0.0269	0.0225	0.0942	-0.0113	0.0243	-0.019	0.1136	0.0123	0.0181	-0.0398	-0.0039	0.2043	0.0124	0.2512	22.2904	27.6366	68.9079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 41
2	X-RAY DIFFRACTION	2	A	42 - 104
3	X-RAY DIFFRACTION	3	A	105 - 162
4	X-RAY DIFFRACTION	4	A	163 - 253
5	X-RAY DIFFRACTION	5	A	254 - 354
6	X-RAY DIFFRACTION	6	A	355 - 455
7	X-RAY DIFFRACTION	7	B	5 - 78
8	X-RAY DIFFRACTION	8	B	79 - 103
9	X-RAY DIFFRACTION	9	B	104 - 145
10	X-RAY DIFFRACTION	10	B	146 - 230
11	X-RAY DIFFRACTION	11	B	231 - 351
12	X-RAY DIFFRACTION	12	B	352 - 455
13	X-RAY DIFFRACTION	13	C	5 - 41
14	X-RAY DIFFRACTION	14	C	42 - 101
15	X-RAY DIFFRACTION	15	C	102 - 166
16	X-RAY DIFFRACTION	16	C	167 - 262
17	X-RAY DIFFRACTION	17	C	263 - 388
18	X-RAY DIFFRACTION	18	C	389 - 455
19	X-RAY DIFFRACTION	19	D	6 - 41
20	X-RAY DIFFRACTION	20	D	42 - 102
21	X-RAY DIFFRACTION	21	D	103 - 128
22	X-RAY DIFFRACTION	22	D	129 - 219
23	X-RAY DIFFRACTION	23	D	220 - 342
24	X-RAY DIFFRACTION	24	D	343 - 455

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