PDB-1xwb: Drospohila thioredoxin, oxidized, P42212

ID or keywords:

Entry

Database: PDB / ID: 1xwb

Title

Drospohila thioredoxin, oxidized, P42212

Components

thioredoxin

Keywords

ELECTRON TRANSPORT / Dimerization / Drosophila melanogaster / redox regulation / thioredoxin / x-ray crystal structure

Function / homology

Function and homology information

The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Protein repair / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / Oxidative Stress Induced Senescence / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis ...
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Wahl, M.C. / Irmler, A. / Hecker, B. / Schirmer, R.H. / Becker, K.

Citation

Journal: J.Mol.Biol. / Year: 2005
Title: Comparative structural analysis of oxidized and reduced thioredoxin from Drosophila melanogaster
Authors: Wahl, M.C. / Irmler, A. / Hecker, B. / Schirmer, R.H. / Becker, K.

History

Deposition	Oct 29, 2004	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 16, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1xwb.cif.gz	99.7 KB	Display	PDBx/mmCIF format
PDB format	pdb1xwb.ent.gz	79 KB	Display	PDB format
PDBx/mmJSON format	1xwb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1xwb_validation.pdf.gz	448.2 KB	Display	wwPDB validaton report
Full document	1xwb_full_validation.pdf.gz	453.6 KB	Display
Data in XML	1xwb_validation.xml.gz	19.5 KB	Display
Data in CIF	1xwb_validation.cif.gz	27.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xw/1xwb ftp://data.pdbj.org/pub/pdb/validation_reports/xw/1xwb	HTTPS FTP

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Related structure data

Related structure data	1xw9C 1xwaC 1xwcC 1aucS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1fb6-1 1xw9-1 1xwa-2 3ziv-2 3ziv-1 1xob-d 1xw9-3 4pol-2 1xlp-2 3hhv-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (4) #91 - Jul 2007 Thymine Dimers similarity (4)

Deposited unit

A: thioredoxin

B: thioredoxin

C: thioredoxin

D: thioredoxin

hetero molecules

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

1

A: thioredoxin

hetero molecules

defined by author&software
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: thioredoxin

hetero molecules

defined by author&software
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: thioredoxin

defined by author&software
11.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: thioredoxin

hetero molecules

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: thioredoxin

hetero molecules

B: thioredoxin

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.465, 99.465, 87.780
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	D-803- CD

#1: Protein	thioredoxin Mass: 11748.636 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TRX-2 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9V429
#2: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.3 Å³/Da / Density % sol: 45.2 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.2 Details: CdCl2, PEG400, pH 5.2, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. obs: 22855 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / B_iso Wilson estimate: 34.4 Å² / R_sym value: 0.042 / Net I/σ(I): 17.2
Reflection shell	Resolution: 2.1→2.2 Å / % possible all: 91.5

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Processing

Software

Name	Version	Classification
REFMAC	5.1.19	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AUC

1auc

Resolution: 2.2→20 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.892 / SU B: 8.744 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.45 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28835	1004	5.1 %	RANDOM
R_work	0.22274	-	-	-
obs	0.22605	18759	86.27 %	-

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: 21.178 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.24 Å²	0 Å²	0 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3264	0	3	218	3485

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3316
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	3012
X-RAY DIFFRACTION	r_angle_refined_deg	1.083	1.972	4484
X-RAY DIFFRACTION	r_angle_other_deg	0.733	3	7044
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.784	5	420
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	532
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3644
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	596
X-RAY DIFFRACTION	r_nbd_refined	0.259	0.2	814
X-RAY DIFFRACTION	r_nbd_other	0.226	0.2	3590
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	2022
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	218
X-RAY DIFFRACTION	r_metal_ion_refined	0.292	0.2	3
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.245	0.2	42
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.23	0.2	104
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.163	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	3.313	4	2112
X-RAY DIFFRACTION	r_mcangle_it	4.384	6	3416
X-RAY DIFFRACTION	r_scbond_it	3.78	4	1204
X-RAY DIFFRACTION	r_scangle_it	5.028	6	1068

LS refinement shell

Resolution: 2.2→2.256 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.373	84
R_work	0.319	1407

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	1.6511	-1.3365	0.6501	12.5481	-4.8726	0.7775	0.0356	0.0544	0.0114	-0.4198	-0.0307	-0.1078	0.1725	-0.0781	-0.0049	0.275	0.0215	0.0453	0.1916	-0.0045	0.2157	31.616	16.2598	11.1134
2	6.3633	0.5609	3.1783	1.3448	1.1952	9.192	-0.0431	-0.4801	-0.0018	0.8064	-0.1826	0.2475	-0.1063	-0.334	0.2257	0.3759	-0.0142	-0.0577	0.1397	0.0114	0.1786	30.4034	17.3108	33.4054
3	0.2997	0.3748	-0.6742	4.3855	-1.3803	1.3306	-0.0025	0.0402	0.0527	-0.3352	-0.2069	-0.4296	0.2925	0.2143	0.2095	0.2244	0.0066	0.0174	0.2336	0.045	0.2994	40.7948	13.5958	17.8319
4	1.3887	-2.1547	5.5242	10.8557	-4.9309	9.6562	-0.027	0.0089	0.3201	0.2574	-0.1429	-0.247	-0.0284	-0.1688	0.1699	0.2338	-0.024	-0.0204	0.1313	0.0012	0.2649	35.3247	29.0356	29.0368
5	0.1261	0.155	-0.2397	0.7694	1.0745	0.6313	0.0114	0.1684	0.1082	0.1056	-0.0746	-0.1359	0.0222	-0.0376	0.0632	0.2492	0.0005	-0.0225	0.2109	0.0282	0.2679	33.4316	20.2416	22.2002
6	2.5536	-2.9172	0.0035	4.5425	2.0155	4.0395	-0.1339	0.042	0.0695	0.1358	-0.0386	0.5129	0.1855	-0.5551	0.1726	0.2354	-0.0526	0.0073	0.25	-0.0321	0.2736	19.2477	90.5928	33.4715
7	6.1326	0.0692	3.4964	7.5502	10.0464	15.0985	-0.0968	0.3017	-0.0912	0.4464	-0.0917	-0.6366	0.059	0.1031	0.1885	0.2201	-0.0157	-0.0424	0.1761	0.1181	0.2423	39.9868	99.1562	32.5278
8	1.2267	-0.3076	-1.1515	0.5129	-2.3811	3.3684	0.1678	-0.2085	0.1859	0.0667	-0.0276	0.5969	-0.162	-0.2059	-0.1403	0.3715	0.0114	0.0187	0.1755	-0.0517	0.173	22.8954	98.9386	40.9623
9	2.698	1.7114	6.8369	14.0463	2.1178	5.8002	-0.4067	0.1384	-0.0004	0.3618	-0.4104	-0.294	0.1457	0.6755	0.8171	0.278	-0.0189	-0.1328	0.218	0.1373	0.1471	39.9408	88.922	40.9057
10	-0.0497	0.1101	0.6641	0.3957	-0.5305	1.1757	-0.0163	-0.01	0.0333	0.1421	-0.1761	-0.0674	-0.0373	-0.032	0.1924	0.3229	-0.0219	-0.0205	0.1931	0.0079	0.2194	30.4682	92.9397	35.7507
11	6.3922	1.1079	-2.3595	7.0286	2.8844	2.8241	0.108	-0.0582	-0.2006	0.1901	-0.0365	0.3375	-0.0064	-0.1083	-0.0715	0.2687	0.0155	0.0216	0.1788	-0.0373	0.2002	71.9738	60.1046	32.2192
12	4.9363	-3.3529	6.1385	5.449	-0.3692	6.2466	0.133	0.2363	0.4204	0.0335	-0.2653	-0.1935	0.1883	0.196	0.1324	0.2198	-0.0133	0.004	0.2077	0.0555	0.246	92.6979	64.6058	25.0699
13	0.3948	1.1035	-1.7776	6.6595	-2.4531	5.2286	-0.2162	-0.219	0.2961	0.3767	0.1967	0.4225	-0.2452	-0.2054	0.0194	0.2674	0.048	-0.0104	0.2235	-0.0269	0.1873	78.9721	67.2479	38.1993
14	11.244	8.5074	-1.4485	9.0526	-2.5078	2.1057	0.1717	0.1924	-0.291	0.3105	-0.2142	-0.5055	0.3698	0.3865	0.0424	0.2496	0.1165	-0.0352	0.1949	0.0568	0.2525	93.3757	54.638	33.6032
15	1.5318	-1.3192	0.3716	1.1353	0.3784	0.6145	-0.0651	-0.0819	0.1228	0.0138	0.0265	0.1232	0.1173	0.0617	0.0386	0.3204	0.0051	-0.0172	0.1746	0.0085	0.1948	83.7325	60.1547	30.975
16	4.3733	3.842	4.0918	-3.5381	5.4452	3.1642	-0.654	-0.1886	-0.0325	-0.5672	0.4542	0.6038	-0.1758	-0.2137	0.1999	0.3306	0.0192	-0.0196	0.1638	0.0086	0.2395	80.6044	83.5087	7.5773
17	8.5128	0.264	-2.1437	10.2142	4.7736	9.8368	0.5283	-0.7696	0.0507	0.7417	-0.3991	-0.2449	-0.2615	0.075	-0.1292	0.2965	-0.0181	-0.0717	0.1262	0.0356	0.1844	88.1223	83.4623	28.633
18	3.677	-1.6906	1.3309	6.1477	-8.2561	14.9109	0.1655	0.3361	0.0345	-0.2465	-0.1433	-0.5953	0.1845	-0.0325	-0.0222	0.223	0.0408	0.0443	0.1934	0.0669	0.2541	91.3862	79.0924	10.4366
19	6.8634	-8.4552	8.6494	18.5886	-8.0147	16.1734	-0.3565	-0.2304	0.9792	0.9847	-0.0947	-1.4341	-1.0636	-0.1179	0.4511	0.2145	-0.1335	-0.0623	0.0874	0.0011	0.3416	92.8632	94.4699	22.5559
20	1.5548	-0.5564	0.438	3.4665	0.4901	2.2126	0.1024	0.0325	0.2157	-0.0186	-0.1233	-0.2565	-0.0914	0.0645	0.0209	0.2262	-0.0235	-0.0026	0.167	0.0283	0.2938	87.0036	86.3251	17.1139

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	93 - 106	93 - 106
2	X-RAY DIFFRACTION	2	A	A	62 - 72	62 - 72
3	X-RAY DIFFRACTION	3	A	A	30 - 50	30 - 50
4	X-RAY DIFFRACTION	4	A	A	6 - 20	6 - 20
5	X-RAY DIFFRACTION	5	A	A	1 - 5	1 - 5
6	X-RAY DIFFRACTION	5	A	A	21 - 29	21 - 29
7	X-RAY DIFFRACTION	5	A	A	51 - 61	51 - 61
8	X-RAY DIFFRACTION	5	A	A	73 - 92	73 - 92
9	X-RAY DIFFRACTION	6	B	B	93 - 106	93 - 106
10	X-RAY DIFFRACTION	7	B	B	62 - 72	62 - 72
11	X-RAY DIFFRACTION	8	B	B	30 - 50	30 - 50
12	X-RAY DIFFRACTION	9	B	B	6 - 20	6 - 20
13	X-RAY DIFFRACTION	10	B	B	2 - 5	2 - 5
14	X-RAY DIFFRACTION	10	B	B	21 - 29	21 - 29
15	X-RAY DIFFRACTION	10	B	B	51 - 61	51 - 61
16	X-RAY DIFFRACTION	10	B	B	73 - 92	73 - 92
17	X-RAY DIFFRACTION	11	C	C	93 - 106	93 - 106
18	X-RAY DIFFRACTION	12	C	C	62 - 72	62 - 72
19	X-RAY DIFFRACTION	13	C	C	30 - 50	30 - 50
20	X-RAY DIFFRACTION	14	C	C	6 - 20	6 - 20
21	X-RAY DIFFRACTION	15	C	C	3 - 5	3 - 5
22	X-RAY DIFFRACTION	15	C	C	21 - 29	21 - 29
23	X-RAY DIFFRACTION	15	C	C	51 - 61	51 - 61
24	X-RAY DIFFRACTION	15	C	C	73 - 92	73 - 92
25	X-RAY DIFFRACTION	16	D	D	93 - 106	93 - 106
26	X-RAY DIFFRACTION	17	D	D	62 - 72	62 - 72
27	X-RAY DIFFRACTION	18	D	D	30 - 50	30 - 50
28	X-RAY DIFFRACTION	19	D	D	6 - 20	6 - 20
29	X-RAY DIFFRACTION	20	D	D	1 - 5	1 - 5
30	X-RAY DIFFRACTION	20	D	D	21 - 29	21 - 29
31	X-RAY DIFFRACTION	20	D	D	51 - 61	51 - 61
32	X-RAY DIFFRACTION	20	D	D	73 - 92	73 - 92

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