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 / cytoplasm
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: To Be Published
Title: 2.3 Angstrom Resolution Crystal Structure of Glutathione Reductase from Vibrio parahaemolyticus in Complex with FAD.
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)

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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u1o.cif.gz	700.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5u1o.ent.gz	580.8 KB	Display	PDB format
PDBx/mmJSON format	5u1o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5u1o_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5u1o_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5u1o_validation.xml.gz	70.9 KB	Display
Data in CIF	5u1o_validation.cif.gz	99.9 KB	Display
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	1gesS S: Starting model for refinement
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

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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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