PDB-4zn0: Structure of the NADPH-dependent thioredoxin reductase from Metha...

ID or keywords:

Entry

Database: PDB / ID: 4zn0

Title

Structure of the NADPH-dependent thioredoxin reductase from Methanosarcina mazei

Components

Thioredoxin reductase

Keywords

OXIDOREDUCTASE /

NADPH /

thioredoxin

Function / homology

Function and homology information

thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals /

cytoplasm
Similarity search - Function

Biological species

Methanosarcina mazei (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Buey, R.M. / de Pereda, J.M. / Balsera, M.

Citation

Journal: Antioxidants (Basel) / Year: 2018
Title: Crystal Structure of the Apo-Form of NADPH-Dependent Thioredoxin Reductase from a Methane-Producing Archaeon.
Authors: Buey, R.M. / Schmitz, R.A. / Buchanan, B.B. / Balsera, M.

History

Deposition	May 4, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zn0.cif.gz	569.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zn0.ent.gz	483.3 KB	Display	PDB format
PDBx/mmJSON format	4zn0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zn/4zn0 ftp://data.pdbj.org/pub/pdb/validation_reports/zn/4zn0	HTTPS FTP

-
Related structure data

Related structure data	3ctyS S: Starting model for refinement
Similar structure data	6o2a-2 5a6d-d 5nfj-d 4nch-d 4b3f-d 3wsx-d 5xz9-1 1xcq-1 4al2-d 5ui2-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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

C: Thioredoxin reductase

D: Thioredoxin reductase

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

1

A: Thioredoxin reductase

C: Thioredoxin reductase

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

2

B: Thioredoxin reductase

D: Thioredoxin reductase

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

Unit cell

Length a, b, c (Å)	117.144, 182.500, 152.046
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Thioredoxin reductase / Mass: 33891.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_2353 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8PUI1, thioredoxin-disulfide reductase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na Acetate pH 4.8, 1.00 M NH4Cl

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 14, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→46.89 Å / Num. all: 50423 / Num. obs: 50353 / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 0.1016 / Net I/σ(I): 29.49
Reflection shell	Resolution: 2.6→2.693 Å / Redundancy: 14.1 % / R_merge(I) obs: 1.196 / Mean I/σ(I) obs: 2.27 / Num. unique all: 3650 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1839	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3CTY

3cty

Resolution: 2.6→46.889 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2407	2410	4.79 %
R_work	0.217	-	-
obs	0.2181	50317	99.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→46.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7954	0	0	68	8022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8167
X-RAY DIFFRACTION	f_angle_d	0.737	11137
X-RAY DIFFRACTION	f_dihedral_angle_d	12.032	2766
X-RAY DIFFRACTION	f_chiral_restr	0.03	1363
X-RAY DIFFRACTION	f_plane_restr	0.003	1431

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.6531	0.321	153	0.3264	2770	X-RAY DIFFRACTION	100
2.6531-2.7108	0.3512	138	0.3168	2806	X-RAY DIFFRACTION	100
2.7108-2.7738	0.2872	161	0.2918	2749	X-RAY DIFFRACTION	100
2.7738-2.8432	0.3421	135	0.3023	2777	X-RAY DIFFRACTION	100
2.8432-2.92	0.3299	125	0.3061	2813	X-RAY DIFFRACTION	100
2.92-3.006	0.3207	122	0.2847	2834	X-RAY DIFFRACTION	100
3.006-3.103	0.2982	139	0.2614	2782	X-RAY DIFFRACTION	100
3.103-3.2138	0.2669	131	0.2431	2791	X-RAY DIFFRACTION	100
3.2138-3.3425	0.2558	146	0.2476	2792	X-RAY DIFFRACTION	100
3.3425-3.4946	0.2886	149	0.2399	2812	X-RAY DIFFRACTION	100
3.4946-3.6787	0.225	141	0.2235	2810	X-RAY DIFFRACTION	100
3.6787-3.9091	0.2049	132	0.2152	2821	X-RAY DIFFRACTION	100
3.9091-4.2108	0.234	130	0.1865	2836	X-RAY DIFFRACTION	100
4.2108-4.6342	0.2025	150	0.1652	2816	X-RAY DIFFRACTION	100
4.6342-5.3039	0.1822	153	0.1749	2847	X-RAY DIFFRACTION	100
5.3039-6.6793	0.2523	152	0.2151	2867	X-RAY DIFFRACTION	100
6.6793-46.8965	0.2231	153	0.1938	2984	X-RAY DIFFRACTION	100

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	2.3454	0.7956	-0.7715	4.2878	-1.631	0.9787	0.1059	-0.1619	-0.0665	0.3666	0.2241	1.1604	-0.1446	-0.9078	-0.001	0.6472	0.0911	0.1151	0.9425	0.1041	0.9469	111.7159	405.1282	168.6676
2	2.4865	-0.4474	0.3335	1.8694	-0.0684	2.9501	-0.0096	0.0318	0.0307	-0.0123	0.0786	0.0612	-0.2219	0.0701	-0	0.4949	-0.024	0.0108	0.5351	0.0307	0.5112	127.3092	416.6737	137.3063
3	1.6181	0.9669	0.2121	1.9356	0.4074	1.6032	-0.0008	-0.0417	-0.1906	0.2817	0.1528	0.0924	0.1359	0.0381	0.002	0.6062	0.0105	0.0533	0.726	0.0437	0.6771	124.8588	403.1837	168.0217
4	4.0377	-1.6361	1.417	1.1362	-1.1859	3.2469	0.055	0.5866	0.2021	-0.2299	-0.1241	-0.3887	-0.1416	0.6672	-0.0006	0.4992	-0.0527	0.0143	0.8275	0.0057	0.6019	156.4362	406.7705	156.7699
5	1.7297	-0.3625	-0.4188	3.1215	-0.3022	2.8691	-0.2546	0.1198	0.4528	0.3502	0.1602	0.0205	-0.7524	-0.0733	-0.0001	0.8437	0.0617	-0.1275	0.5139	-0.0202	0.7541	129.8114	433.9686	157.1556
6	2.8507	0.3879	0.9815	1.4608	0.0414	2.5881	-0.0562	0.0533	-0.0584	0.3228	0.0514	0.0988	0.0158	-0.1403	-0	0.5179	-0.0492	-0.0143	0.6686	-0.0267	0.5338	144.7776	404.5506	163.1141
7	1.4542	0.3388	1.8394	3.3495	-0.4647	2.5642	0.0829	0.0138	-0.3697	-0.3909	0.1663	0.7321	0.8796	-0.1415	-0.0005	0.9352	-0.0185	-0.216	0.6099	0.0601	0.9401	118.7252	385.2955	133.7947
8	0.2772	0.3266	-0.039	1.4986	-1.7347	5.2678	0.3492	-0.098	-0.1638	-0.0747	-0.0184	0.1599	0.9917	0.0619	0.0049	0.7931	-0.0571	-0.1547	0.5751	0.0237	0.796	127.3715	378.1188	164.2358
9	1.6324	-0.3362	0.1728	1.1813	-0.098	0.0957	0.0791	0.0103	0.0081	0.1768	-0.045	-0.4596	0.1018	0.5448	-0	0.801	0.0094	-0.0687	0.7094	0.0268	0.698	129.9583	392.759	139.0549
10	0.9914	0.0043	0.9457	1.8744	-0.9951	1.4233	-0.6361	-0.3484	0.4727	0.3365	-0.0148	-0.3207	-1.2483	0.2168	-0.0003	1.2822	0.1133	-0.2564	0.95	-0.1123	0.9449	145.6321	436.4377	185.985
11	1.6702	-0.5253	0.6	3.1472	0.3627	4.2909	0.1169	-0.2686	-0.0688	0.2015	-0.1516	0.0726	0.0245	-0.2233	0.0001	0.538	-0.05	-0.0205	0.6089	-0.0182	0.5423	152.8225	399.9628	188.7503
12	1.5165	0.3416	-0.3409	0.6555	-0.6	0.6433	-0.506	-0.2812	-0.1112	0.3027	0.4767	0.3864	-0.4825	-0.2627	0.0001	1.1535	0.1866	-0.1139	0.9215	-0.0808	0.8582	135.873	427.3588	182.8979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 244 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 245 through 307 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 114 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 115 through 244 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 245 through 307 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 103 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 104 through 264 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 265 through 307 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 2 through 114 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 115 through 244 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 245 through 306 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi