PDB-2q0k: Oxidized thioredoxin reductase from Helicobacter pylori in comple...

ID or keywords:

Entry

Database: PDB / ID: 2q0k

Title

Oxidized thioredoxin reductase from Helicobacter pylori in complex with NADP+

Components

Thioredoxin reductase

Keywords

OXIDOREDUCTASE / bacterial thioredoxin reductase / Helicobacter pylori / NADP+ binding

Function / homology

Function and homology information

thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytosol
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Sandalova, T. / Gustafsson, T. / Lu, J. / Holmgren, A. / Schneider, G.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: High-resolution structures of oxidized and reduced thioredoxin reductase from Helicobacter pylori.
Authors: Gustafsson, T.N. / Sandalova, T. / Lu, J. / Holmgren, A. / Schneider, G.

History

Deposition	May 22, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2q0k.cif.gz	144.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2q0k.ent.gz	112.7 KB	Display	PDB format
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Validation report

Summary document	2q0k_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	2q0k_full_validation.pdf.gz	1.4 MB	Display
Data in XML	2q0k_validation.xml.gz	16.5 KB	Display
Data in CIF	2q0k_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/2q0k ftp://data.pdbj.org/pub/pdb/validation_reports/q0/2q0k	HTTPS FTP

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Related structure data

Related structure data	2q0lC 1tdeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3ish-1 3ish-2 1trb-1 5mh4-1 5mis-1 3d8x-d 5utx-d 5m5j-d 5miq-1 1vdc-1 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: Thioredoxin reductase

B: Thioredoxin reductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.128, 99.195, 64.436
Angle α, β, γ (deg.)	90.00, 100.02, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 5 / Auth seq-ID: 1 - 310 / Label seq-ID: 1 - 310

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

Details

The biological assembly is a dimer

#1: Protein	Thioredoxin reductase / TRXR Mass: 33577.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: trxB / Plasmid: pPROK/TR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P56431, thioredoxin-disulfide reductase
#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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.35 Å³/Da / Density % sol: 47.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 22% PEG 3350, 0.1M MIB pH 6.0, 8mM pentaethylene glycol monooctyl ether, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9393 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006
Radiation	Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9393 Å / Relative weight: 1
Reflection	Resolution: 1.7→63.5 Å / Num. all: 66999 / Num. obs: 66999 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.059 / R_sym value: 0.059 / Net I/σ(I): 5.4
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.429 / Mean I/σ(I) obs: 1.7 / R_sym value: 0.429 / % possible all: 90.2

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Processing

Software

Name	Version	Classification
SCALA		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
ADSC	Quantum	data collection
MOSFLM		data reduction
REFMAC	5.2.0019	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TDE

1tde

Resolution: 1.7→63.5 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.938 / SU B: 5.202 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22605	3364	5 %	RANDOM
R_work	0.18834	-	-	-
obs	0.19024	63605	98.32 %	-
all	-	66969	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 23.304 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.79 Å²	0 Å²	0.91 Å²
2-	-	-2.18 Å²	0 Å²
3-	-	-	1.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→63.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4688	0	202	357	5247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4998
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3314
X-RAY DIFFRACTION	r_angle_refined_deg	1.604	2.011	6782
X-RAY DIFFRACTION	r_angle_other_deg	0.858	3.005	8002
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.378	5	618
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.254	24.848	198
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.722	15	824
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.184	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.165	0.2	756
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5496
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	962
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	986
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	3567
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	2479
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	2568
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	299
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	0.23	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.186	0.2	39
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.193	0.2	13
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	0.814	1.5	3952
X-RAY DIFFRACTION	r_mcbond_other	0.226	1.5	1288
X-RAY DIFFRACTION	r_mcangle_it	0.984	2	4878
X-RAY DIFFRACTION	r_scbond_it	1.746	3	2354
X-RAY DIFFRACTION	r_scangle_it	2.306	4.5	1904
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1816	medium positional	0.4	0.5
2146	loose positional	0.72	5
1816	medium thermal	1.43	2
2146	loose thermal	1.7	10

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.298	217	-
R_work	0.248	4012	-
obs	-	-	84.44 %

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	1.382	-0.3847	-0.3602	5.4322	-1.1019	1.772	-0.0453	0.1418	0.196	-0.4638	0.1773	0.6224	0.0788	-0.1491	-0.1319	-0.028	-0.057	-0.1589	0.0776	0.0454	-0.1297	2.94	-5.681	11.444
2	3.6457	3.9778	-0.3534	14.4315	0.6737	4.6979	-0.1346	0.0772	0.1881	-0.6267	0.2828	0.8388	-0.0846	-0.3598	-0.1482	-0.0841	-0.0404	-0.2153	0.0907	0.0701	-0.1433	0.643	-5.492	8.087
3	4.7791	0.9539	-0.9932	4.8901	1.0334	2.3072	-0.006	0.0166	0.1979	0.0332	-0.0358	0.6162	-0.0218	-0.1478	0.0418	-0.13	0.0086	-0.0515	0.0488	0.0382	0.0273	-4.105	-0.799	29.579
4	2.1001	-0.3897	0.0682	2.067	1.0569	1.5096	-0.036	0.2836	0.1968	-0.3914	0.0708	0.7076	-0.0705	-0.5099	-0.0348	-0.0643	-0.0232	-0.1706	0.1182	0.1013	0.0508	-5.102	-0.218	14.975
5	2.1901	1.6976	-0.0749	5.2375	-0.7559	4.9748	-0.2422	0.2762	-0.1012	-0.9523	0.3174	0.4433	0.2289	-0.1715	-0.0752	0.1192	-0.0733	-0.192	0.0544	0.0062	-0.1568	3.029	-17.984	8.016
6	2.0809	0.1066	0.1617	2.4962	0.137	1.989	0.0451	0.1209	0.2687	-0.0363	0.0273	0.2499	0.007	-0.0621	-0.0724	-0.0459	-0.0288	-0.0228	0.0273	0.0226	-0.1198	-2.117	-12.46	41.215
7	3.9808	-0.3464	0.0638	2.4514	-0.0049	1.8064	0.0502	-0.2246	0.1151	0.2106	0.0323	0.1096	0.1067	0.1	-0.0825	-0.0437	-0.017	-0.0258	-0.0001	-0.028	-0.2018	3.174	-17.807	49.301
8	4.8196	0.8792	-1.5661	2.7139	0.0217	2.3344	0.0847	-0.3014	0.0167	0.1238	-0.0405	0.1391	0.1557	-0.0508	-0.0442	-0.0238	-0.0298	-0.0505	0.0164	0.0049	-0.1503	-3.363	-19.845	48.549
9	5.7582	2.1939	-2.8288	6.9247	-1.0394	5.9023	-0.4423	0.047	-0.6389	-0.441	0.3268	-0.0137	0.9069	0.0725	0.1155	0.1482	0.0122	-0.0628	0.0051	-0.017	-0.115	9.309	-24.497	15.656
10	1.159	-0.0757	-0.2587	2.9463	-0.1422	1.6731	-0.0321	0.0039	0.0264	-0.1835	0.1396	-0.0929	0.1149	0.1613	-0.1076	-0.0364	-0.0118	-0.0713	0.0626	-0.0153	-0.1165	12.928	-9.398	17.88
11	0.179	0.4118	1.2494	8.3057	4.9696	9.3175	0.0005	-0.0328	0.1783	0.1683	-0.041	0.6017	0.4459	-0.4601	0.0405	-0.0396	-0.0406	-0.0364	0.0907	0.0099	-0.0168	0.162	-10.123	25.282
12	10.0051	4.9935	1.9293	16.9819	2.2562	6.4836	-0.6829	0.6391	-0.8078	-1.0986	0.5704	-1.72	-0.051	0.8744	0.1125	0.2464	-0.0456	0.005	0.2399	-0.0431	-0.0489	8.086	-22.739	37.945
13	2.1275	0.9289	0.1408	1.4375	-0.6322	2.036	0.0685	-0.0918	0.3677	0.2451	-0.0542	0.2331	-0.1097	-0.105	-0.0143	-0.0341	0.0094	-0.0354	0.0275	-0.0341	-0.0491	13.713	9.504	36.646
14	1.6884	0.1771	0.4791	1.3517	-0.1738	2.0259	-0.0145	-0.0261	0.3844	0.0144	0.0499	0.2674	-0.1862	-0.1979	-0.0354	-0.104	0.0334	-0.0388	0.0139	0.0217	0.0632	4.147	12.776	27.498
15	2.4985	1.0143	0.1799	3.3886	-0.8448	3.2805	0.1497	-0.0928	0.1808	0.352	-0.0978	-0.1464	-0.1371	0.1518	-0.0519	-0.0667	-0.0125	-0.0672	0.0202	-0.0284	-0.0846	26.05	11.839	38.53
16	5.5271	4.1012	2.0961	5.3734	1.7125	2.4784	0.2731	-0.6849	0.1667	0.1962	-0.4581	0.5728	0.1657	-0.4946	0.185	-0.0474	-0.0208	-0.0897	0.1905	0.0355	-0.1208	12.073	18.266	6.806
17	6.8199	-0.0464	2.2408	6.8638	-1.6827	6.7314	0.4254	-0.1449	-1.2253	-0.3169	0.1289	-0.0577	0.6845	-0.2041	-0.5543	-0.0223	-0.0521	-0.1433	0.0346	0.0684	-0.0123	17.836	9.96	-0.115
18	13.7705	2.1245	-0.8475	5.7408	0.2503	6.8767	0.141	0.3685	-2.403	-0.2346	0.3527	-0.9647	1.0833	1.2454	-0.4937	0.2232	0.1298	-0.0889	0.1781	-0.0713	0.4073	27.044	7.265	-2.497
19	6.2209	0.6948	1.9887	9.6243	7.2456	11.8023	-0.3202	0.0909	0.3397	-1.0155	-0.1999	0.2737	-1.1816	-0.3943	0.5201	0.0185	0.0095	-0.173	0.0389	0.0728	-0.2494	18.03	23.141	-2.09
20	2.3992	-0.4272	3.295	4.3415	-1.8406	12.9058	-0.1941	0.1124	-0.0038	-0.2528	-0.4357	-0.1921	-0.7386	0.3799	0.6298	-0.0452	-0.0427	-0.131	0.0922	0.0634	-0.2044	19.953	20.715	-0.331
21	6.5603	0.1852	1.4752	2.6201	-0.5409	0.7059	-0.0501	0.2442	0.2394	-0.2497	0.0538	-0.4935	0.0092	0.0854	-0.0037	-0.1238	-0.0224	-0.0307	0.0844	-0.0176	-0.0021	33.39	9.408	30.06
22	1.7298	0.613	0.4914	1.7325	0.1288	1.3917	0.0621	0.125	-0.0881	-0.0132	0.0401	-0.0852	0.1088	0.1329	-0.1022	-0.0671	0.0116	-0.0567	0.0524	-0.0288	-0.0707	20.58	0.402	28.259
23	3.7217	1.9574	5.9538	2.7943	1.6888	10.7036	-0.0849	0.2093	0.7057	0.0353	0.013	0.2203	-0.1518	0.1933	0.072	-0.0967	0.0017	-0.0713	0.0674	0.0466	0.0555	15.111	13.1	23.034
24	26.2018	-0.3733	4.7859	0.3595	1.5486	8.2541	0.6618	-1.2703	-3.622	0.3024	0.1771	-1.4388	1.203	0.3812	-0.8389	0.2882	0.0258	-0.2102	0.3439	0.2181	0.5361	28.101	11.073	8.212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 21	1 - 21
2	X-RAY DIFFRACTION	2	A	A	22 - 33	22 - 33
3	X-RAY DIFFRACTION	3	A	A	34 - 59	34 - 59
4	X-RAY DIFFRACTION	4	A	A	60 - 77	60 - 77
5	X-RAY DIFFRACTION	5	A	A	78 - 114	78 - 114
6	X-RAY DIFFRACTION	6	A	A	115 - 157	115 - 157
7	X-RAY DIFFRACTION	7	A	A	158 - 218	158 - 218
8	X-RAY DIFFRACTION	8	A	A	219 - 239	219 - 239
9	X-RAY DIFFRACTION	9	A	A	240 - 256	240 - 256
10	X-RAY DIFFRACTION	10	A	A	258 - 310	258 - 310
11	X-RAY DIFFRACTION	11	A	C	400
12	X-RAY DIFFRACTION	12	A	D	401
13	X-RAY DIFFRACTION	13	B	B	1 - 39	1 - 39
14	X-RAY DIFFRACTION	14	B	B	40 - 77	40 - 77
15	X-RAY DIFFRACTION	15	B	B	78 - 114	78 - 114
16	X-RAY DIFFRACTION	16	B	B	115 - 148	115 - 148
17	X-RAY DIFFRACTION	17	B	B	149 - 173	149 - 173
18	X-RAY DIFFRACTION	18	B	B	174 - 193	174 - 193
19	X-RAY DIFFRACTION	19	B	B	194 - 218	194 - 218
20	X-RAY DIFFRACTION	20	B	B	219 - 240	219 - 240
21	X-RAY DIFFRACTION	21	B	B	241 - 256	241 - 256
22	X-RAY DIFFRACTION	22	B	B	257 - 310	257 - 310
23	X-RAY DIFFRACTION	23	B	E	400
24	X-RAY DIFFRACTION	24	B	F	401

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Yorodumi