PDB-4x43: Structure of proline-free E. coli Thioredoxin

ID or keywords:

Entry

Database: PDB / ID: 4x43

Title

Structure of proline-free E. coli Thioredoxin

Components

Thioredoxin-1

Keywords

OXIDOREDUCTASE /

Protein folding / THIOREDOXIN FOLD /

PROTEIN DISULFIDE OXIDOREDUCTASE ACTIVITY /

REDOX PROTEIN

Function / homology

Function and homology information

DNA polymerase processivity factor activity /

protein-disulfide reductase activity / cell redox homeostasis /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Scharer, M.A. / Glockshuber, R.

Funding support

Switzerland, 2items

Citation

Journal: Sci Rep / Year: 2015
Title: Acceleration of protein folding by four orders of magnitude through a single amino acid substitution.
Authors: Roderer, D.J. / Scharer, M.A. / Rubini, M. / Glockshuber, R.

History

Deposition	Dec 2, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 8, 2015	Group: Database references
Revision 2.0	Sep 6, 2017	Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / software Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1	Oct 11, 2017	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x43.cif.gz	143.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4x43.ent.gz	112 KB	Display	PDB format
PDBx/mmJSON format	4x43.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/x4/4x43 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/4x43	HTTPS FTP

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Related structure data

Related structure data	4hu7S S: Starting model for refinement
Similar structure data	5jy5-2 5j7d-1 1ti3-d 6q6v-1 5j7d-2 5nyl-2 5dqy-d 6q6v-2 2lrc-d 5ykw-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4hu7S

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	#91 - Jul 2007 Thymine Dimers similarity (5) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (4)

Deposited unit

A: Thioredoxin-1

B: Thioredoxin-1

C: Thioredoxin-1

34.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioredoxin-1

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

2

B: Thioredoxin-1

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

3

C: Thioredoxin-1

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

Unit cell

Length a, b, c (Å)	34.670, 48.570, 89.940
Angle α, β, γ (deg.)	90.000, 101.010, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Thioredoxin-1 / / Trx-1 / Trx0P Mass: 11557.201 Da / Num. of mol.: 3 / Mutation: P34A, P40A, P64A, P68A, P76A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trxA, fipA, tsnC, b3781, JW5856 / Plasmid: pTRX0P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AA25
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Thioredoxin-1 /

/ Trx-1 / Trx0P

Mass: 11557.201 Da / Num. of mol.: 3 / Mutation: P34A, P40A, P64A, P68A, P76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Gene: trxA, fipA, tsnC, b3781, JW5856 / Plasmid: pTRX0P / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AA25

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.14 Å³/Da / Density % sol: 42.63 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 0.97941 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2013

Radiation

Monochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97941 Å / Relative weight: 1

Reflection

Resolution: 1.65→44.1 Å / Num. obs: 35498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / B_iso Wilson estimate: 20.83 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.139 / R_rim(I) all: 0.145 / Χ²: 0.93 / Net I/σ(I): 14.04 / Num. measured all: 437002

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.65-1.69		0.4	2.031	1.14	30727	2588	2577	2.12	99.6
1.69-1.74		0.494	1.736	1.36	30993	2573	2572	1.811	100
1.74-1.79		0.635	1.416	1.73	30010	2443	2448	1.476	100
1.79-1.84		0.748	1.149	2.18	29445	2409	2402	1.199	99.7
1.84-1.91		0.822	0.915	2.82	28445	2312	2316	0.954	100
1.91-1.97		0.884	0.677	3.73	26038	2268	2261	0.708	99.7
1.97-2.05		0.932	0.532	4.93	26753	2216	2219	0.556	100
2.05-2.13		0.954	0.443	6.3	27447	2094	2094	0.461	100
2.13-2.22		0.976	0.33	8.28	26040	2004	2000	0.344	99.8
2.22-2.33		0.981	0.258	10.54	24772	1920	1921	0.268	100
2.33-2.46		0.99	0.212	12.46	23520	1835	1838	0.22	100
2.46-2.61		0.993	0.17	15.17	21393	1732	1728	0.178	99.8
2.61-2.79		0.993	0.138	17.75	18609	1624	1625	0.144	100
2.79-3.01		0.997	0.101	24.27	18879	1554	1552	0.105	99.9
3.01-3.3		0.999	0.073	33.76	18277	1398	1398	0.076	100
3.3-3.69		0.999	0.056	43.63	16193	1268	1268	0.058	100
3.69-4.26		0.999	0.042	52.91	14382	1160	1161	0.044	100
4.26-5.22		0.999	0.036	56.58	10583	940	937	0.037	99.7
5.22-7.38		0.999	0.04	54.36	9225	756	755	0.042	99.9
	7.38	1	0.026	77.57	5271	430	427	0.027	99.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.63 Å	44.14 Å
Translation	2.63 Å	44.14 Å

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling
Coot		model building
PDB_EXTRACT	3.14	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4hu7

4hu7

Resolution: 1.65→44.1 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2179	924	2.6 %
R_work	0.1758	34574	-
obs	0.1769	35498	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 89.92 Å² / B_iso mean: 28.9816 Å² / B_iso min: 12.29 Å²

Refinement step

Cycle: final / Resolution: 1.65→44.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2416	0	0	284	2700
B_iso mean	-	-	-	34.26	-
Num. residues	-	-	-	-	321

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2505
X-RAY DIFFRACTION	f_angle_d	1.016	3392
X-RAY DIFFRACTION	f_chiral_restr	0.045	400
X-RAY DIFFRACTION	f_plane_restr	0.004	432
X-RAY DIFFRACTION	f_dihedral_angle_d	12.377	889

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.6501-1.7371	0.346	108	0.2883	4924	5032
1.7371-1.8459	0.286	118	0.2579	4889	5007
1.8459-1.9885	0.2473	144	0.2168	4899	5043
1.9885-2.1886	0.2222	132	0.1946	4927	5059
2.1886-2.5052	0.2374	141	0.1861	4939	5080
2.5052-3.1562	0.2478	144	0.177	4953	5097
3.1562-44.1585	0.1671	137	0.1352	5043	5180

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	3.4009	0.9619	-2.3118	5.5041	-0.1873	6.983	0.1599	-0.2695	-0.0945	0.3757	-0.504	0.6185	0.4368	-1.0092	0.1802	0.2138	-0.1116	0.0365	0.3856	-0.0583	0.2457	-22.3966	-2.6857	-21.9685
2	3.8047	0.5321	0.1551	3.8429	-1.4049	6.5172	0.1433	-0.2613	0.0156	0.1994	-0.0841	0.0178	0.1575	-0.1585	-0.0418	0.1485	-0.023	0.0001	0.1286	-0.0179	0.1138	-12.3714	-0.0658	-20.8245
3	7.3101	3.3964	-6.1394	6.5965	-3.3074	6.8367	0.0263	-0.1182	-0.5027	-0.0382	-0.1618	-0.3751	0.8844	0.1273	0.0696	0.3274	-0.0307	-0.0614	0.2077	-0.0384	0.1957	-7.0743	-8.3314	-24.2994
4	4.7856	2.6137	4.0607	9.4977	4.9814	6.421	-0.2862	-0.0679	0.3275	-0.0066	-0.0932	0.306	-0.6135	-0.1425	0.39	0.2485	0.0113	-0.0019	0.1606	-0.0163	0.2062	-14.8064	7.7336	-26.664
5	3.8301	1.142	-0.8722	5.0263	-4.2896	7.527	0.0248	0.0964	-0.0696	-0.2378	-0.0222	-0.1394	0.852	0.1312	0.0184	0.3429	0.0241	-0.0237	0.2517	0.0156	0.1654	-3.2785	-6.2293	-14.2199
6	4.4873	1.299	-1.5574	3.1458	1.3239	5.6638	-0.048	-0.0849	-0.1241	0.2124	-0.0011	-0.1991	0.2974	0.1234	0.0642	0.1342	0.0136	-0.0166	0.0894	0.0152	0.2569	1.9527	-20.6076	-38.552
7	5.6708	0.7805	2.7243	4.3857	2.4255	4.1809	0.1434	-0.1548	0.0365	0.1369	-0.146	-0.0797	0.091	-0.205	-0.0108	0.0687	-0.0158	0.0207	0.096	0.0179	0.1638	0.9472	-10.1053	-39.3123
8	5.4835	-1.8511	1.4963	3.492	-0.8875	3.4326	-0.1111	0.4009	0.1163	-0.2794	-0.0353	-0.1736	0.0464	0.1597	0.1372	0.1476	-0.0324	0.0357	0.1168	-0.0414	0.2707	6.0083	-9.2428	-48.4455
9	5.2115	-0.832	0.9418	8.7138	4.039	3.9757	0.0045	-0.2157	0.1568	0.0639	-0.1449	0.8627	-0.2508	-0.4268	0.1349	0.1614	0.0183	0.0581	0.1624	0.0097	0.2671	-9.4361	-11.3388	-38.2209
10	2.9024	-0.026	0.7352	3.9254	-1.8666	6.9687	-0.073	0.0496	0.2571	-0.1953	0.1558	-0.078	0.0602	0.0284	-0.0731	0.1237	-0.0227	0.0027	0.0924	-0.0014	0.2138	10.4815	-2.7867	-42.162
11	2.4604	0.5135	2.2725	8.4603	0.8939	9.1373	-0.2675	0.3395	-0.0317	-0.9529	0.2152	-0.5848	-0.3673	0.5242	0.1722	0.3467	-0.0559	0.0422	0.3409	-0.0003	0.2543	0.5422	18.3584	-18.1936
12	7.5374	-0.055	1.3234	2.8721	-1.2326	2.753	0.0825	0.1465	-0.1118	-0.1404	-0.1048	0.1157	0.1222	-0.1124	0.0299	0.2477	-0.0242	-0.0336	0.2203	-0.056	0.1413	-3.4794	14.6399	-9.4436
13	2.3836	-0.5888	0.5375	1.3117	0.1618	1.9948	-0.0626	-0.2754	0.2083	0.0587	0.0271	-0.0579	-0.1974	-0.0094	0.0656	0.2664	-0.0215	-0.0131	0.2332	-0.0337	0.1857	-0.0019	22.0594	-2.9055
14	6.4987	-3.6218	0.9096	7.1581	0.4893	6.7031	-0.1194	0.2469	-0.0187	0.4214	-0.1527	0.2159	-0.0621	-0.7659	0.3069	0.2346	-0.0019	-0.0366	0.2793	-0.074	0.1753	-12.3603	14.1112	-14.5362
15	7.4389	2.301	4.9173	6.5929	-0.6409	4.7248	0.2988	-0.2828	-0.3446	0.3571	-0.0254	-0.4225	0.4553	0.008	-0.2556	0.3074	-0.0344	-0.0454	0.2154	0.0003	0.1369	2.3054	13.0629	1.4653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 21 )	A	0
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	A	22
3	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	A	54
4	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	A	75
5	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 53 )	A	0
6	X-RAY DIFFRACTION	4	chain 'A' and (resid 61 through 74 )	A	0
7	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 108 )	A	0
8	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 21 )	B	0
9	X-RAY DIFFRACTION	7	chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	B	22
10	X-RAY DIFFRACTION	7	chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	B	54
11	X-RAY DIFFRACTION	7	chain 'B' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	B	75
12	X-RAY DIFFRACTION	8	chain 'B' and (resid 31 through 53 )	B	0
13	X-RAY DIFFRACTION	9	chain 'B' and (resid 61 through 74 )	B	0
14	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 108 )	B	0
15	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 21 )	C	0
16	X-RAY DIFFRACTION	12	chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	C	22
17	X-RAY DIFFRACTION	12	chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	C	54
18	X-RAY DIFFRACTION	12	chain 'C' and (resid 22 through 30 or resid 54 through 60 or resid 75 through 91)	C	75
19	X-RAY DIFFRACTION	13	chain 'C' and (resid 31 through 53 )	C	0
20	X-RAY DIFFRACTION	14	chain 'C' and (resid 61 through 74 )	C	0
21	X-RAY DIFFRACTION	15	chain 'C' and (resid 92 through 108 )	C	0

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