[English] 日本語
Yorodumi
- PDB-6utl: Yeast Thiol Specific antoxidant 2 with C171S mutation and catalyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6utl
TitleYeast Thiol Specific antoxidant 2 with C171S mutation and catalytic cysteine alkylated with iodoacetamide
ComponentsPeroxiredoxin TSA2
KeywordsOXIDOREDUCTASE / Peroxiredoxin / 2-Cys Prx / Peroxidase / Iodoacetamide
Function / homology
Function and homology information


NFE2L2 regulating anti-oxidant/detoxification enzymes / TP53 Regulates Metabolic Genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / peroxiredoxin activity / cell redox homeostasis / hydrogen peroxide catabolic process / protein folding / cellular response to oxidative stress / response to oxidative stress ...NFE2L2 regulating anti-oxidant/detoxification enzymes / TP53 Regulates Metabolic Genes / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / peroxiredoxin activity / cell redox homeostasis / hydrogen peroxide catabolic process / protein folding / cellular response to oxidative stress / response to oxidative stress / protein stabilization / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTairum, C.A. / Bannitz-Fernandes, R. / Tonoli, C.C.C. / Murakami, M.T. / de Oliveira, M.A. / Netto, L.E.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia13/07937-8 Brazil
CitationJournal: Free Radic Biol Med / Year: 2020
Title: Reduction of sulfenic acids by ascorbate in proteins, connecting thiol-dependent to alternative redox pathways.
Authors: Anschau, V. / Ferrer-Sueta, G. / Aleixo-Silva, R.L. / Bannitz Fernandes, R. / Tairum, C.A. / Tonoli, C.C.C. / Murakami, M.T. / de Oliveira, M.A. / Netto, L.E.S.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin TSA2
B: Peroxiredoxin TSA2
C: Peroxiredoxin TSA2
D: Peroxiredoxin TSA2
E: Peroxiredoxin TSA2
F: Peroxiredoxin TSA2
G: Peroxiredoxin TSA2
H: Peroxiredoxin TSA2
I: Peroxiredoxin TSA2
J: Peroxiredoxin TSA2


Theoretical massNumber of molelcules
Total (without water)238,53210
Polymers238,53210
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16790 Å2
ΔGint-72 kcal/mol
Surface area67620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.365, 177.306, 115.262
Angle α, β, γ (deg.)90.000, 103.280, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 16421 - 184
21METMETLYSLYSBB1 - 16421 - 184
12METMETASNASNAA1 - 16521 - 185
22METMETASNASNCC1 - 16521 - 185
13METMETLYSLYSAA1 - 16421 - 184
23METMETLYSLYSDD1 - 16421 - 184
14VALVALLYSLYSAA2 - 16422 - 184
24VALVALLYSLYSEE2 - 16422 - 184
15METMETLYSLYSAA1 - 16421 - 184
25METMETLYSLYSFF1 - 16421 - 184
16VALVALASNASNAA2 - 16522 - 185
26VALVALASNASNGG2 - 16522 - 185
17METMETTHRTHRAA1 - 16721 - 187
27METMETTHRTHRHH1 - 16721 - 187
18VALVALASPASPAA2 - 16322 - 183
28VALVALASPASPII2 - 16322 - 183
19VALVALLYSLYSAA2 - 16422 - 184
29VALVALLYSLYSJJ2 - 16422 - 184
110METMETLYSLYSBB1 - 16421 - 184
210METMETLYSLYSCC1 - 16421 - 184
111METMETASNASNBB1 - 16521 - 185
211METMETASNASNDD1 - 16521 - 185
112VALVALLYSLYSBB2 - 16422 - 184
212VALVALLYSLYSEE2 - 16422 - 184
113METMETASNASNBB1 - 16521 - 185
213METMETASNASNFF1 - 16521 - 185
114VALVALLYSLYSBB2 - 16422 - 184
214VALVALLYSLYSGG2 - 16422 - 184
115METMETLYSLYSBB1 - 16421 - 184
215METMETLYSLYSHH1 - 16421 - 184
116VALVALASPASPBB2 - 16322 - 183
216VALVALASPASPII2 - 16322 - 183
117VALVALLYSLYSBB2 - 16422 - 184
217VALVALLYSLYSJJ2 - 16422 - 184
118METMETLYSLYSCC1 - 16421 - 184
218METMETLYSLYSDD1 - 16421 - 184
119VALVALLYSLYSCC2 - 16422 - 184
219VALVALLYSLYSEE2 - 16422 - 184
120METMETLYSLYSCC1 - 16421 - 184
220METMETLYSLYSFF1 - 16421 - 184
121VALVALASNASNCC2 - 16522 - 185
221VALVALASNASNGG2 - 16522 - 185
122METMETASNASNCC1 - 16521 - 185
222METMETASNASNHH1 - 16521 - 185
123VALVALASPASPCC2 - 16322 - 183
223VALVALASPASPII2 - 16322 - 183
124VALVALLYSLYSCC2 - 16422 - 184
224VALVALLYSLYSJJ2 - 16422 - 184
125VALVALLYSLYSDD2 - 16422 - 184
225VALVALLYSLYSEE2 - 16422 - 184
126METMETASNASNDD1 - 16521 - 185
226METMETASNASNFF1 - 16521 - 185
127VALVALLYSLYSDD2 - 16422 - 184
227VALVALLYSLYSGG2 - 16422 - 184
128METMETLYSLYSDD1 - 16421 - 184
228METMETLYSLYSHH1 - 16421 - 184
129VALVALASPASPDD2 - 16322 - 183
229VALVALASPASPII2 - 16322 - 183
130VALVALLYSLYSDD2 - 16422 - 184
230VALVALLYSLYSJJ2 - 16422 - 184
131VALVALLYSLYSEE2 - 16422 - 184
231VALVALLYSLYSFF2 - 16422 - 184
132VALVALLYSLYSEE2 - 16422 - 184
232VALVALLYSLYSGG2 - 16422 - 184
133VALVALLYSLYSEE2 - 16422 - 184
233VALVALLYSLYSHH2 - 16422 - 184
134VALVALASPASPEE2 - 16322 - 183
234VALVALASPASPII2 - 16322 - 183
135VALVALASNASNEE2 - 16522 - 185
235VALVALASNASNJJ2 - 16522 - 185
136VALVALLYSLYSFF2 - 16422 - 184
236VALVALLYSLYSGG2 - 16422 - 184
137METMETLYSLYSFF1 - 16421 - 184
237METMETLYSLYSHH1 - 16421 - 184
138VALVALASPASPFF2 - 16322 - 183
238VALVALASPASPII2 - 16322 - 183
139VALVALLYSLYSFF2 - 16422 - 184
239VALVALLYSLYSJJ2 - 16422 - 184
140VALVALASNASNGG2 - 16522 - 185
240VALVALASNASNHH2 - 16522 - 185
141VALVALASPASPGG2 - 16322 - 183
241VALVALASPASPII2 - 16322 - 183
142VALVALLYSLYSGG2 - 16422 - 184
242VALVALLYSLYSJJ2 - 16422 - 184
143VALVALASPASPHH2 - 16322 - 183
243VALVALASPASPII2 - 16322 - 183
144VALVALLYSLYSHH2 - 16422 - 184
244VALVALLYSLYSJJ2 - 16422 - 184
145VALVALASPASPII2 - 16322 - 183
245VALVALASPASPJJ2 - 16322 - 183

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

-
Components

#1: Protein
Peroxiredoxin TSA2 / Prx / Cytoplasmic thiol peroxidase 2 / cTPx 2 / Thiol-specific antioxidant protein 2 / Thioredoxin ...Prx / Cytoplasmic thiol peroxidase 2 / cTPx 2 / Thiol-specific antioxidant protein 2 / Thioredoxin peroxidase type Ib / TPx type Ib


Mass: 23853.172 Da / Num. of mol.: 10
Mutation: C171S, peroxidatic C48 alkylated with iodoacetamide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TSA2, YDR453C, D9461.38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04120, peroxiredoxin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 % w/v PEG 6000, 5 % v/v 2-Methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.733
11-H, -K, H+L20.267
ReflectionResolution: 2.6→47.4 Å / Num. obs: 62339 / % possible obs: 97.9 % / Redundancy: 2.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.149 / Net I/σ(I): 6.6
Reflection shellResolution: 2.61→2.76 Å / Rmerge(I) obs: 1.751 / Num. unique obs: 9992 / CC1/2: 0.236 / Rrim(I) all: 2.169

-
Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVB
Resolution: 2.6→47.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.275 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 3018 4.8 %RANDOM
Rwork0.198 ---
obs0.1995 59320 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.84 Å2 / Biso mean: 74.058 Å2 / Biso min: 46.54 Å2
Baniso -1Baniso -2Baniso -3
1--8.36 Å20 Å216.23 Å2
2---37.66 Å2-0 Å2
3---46.02 Å2
Refinement stepCycle: final / Resolution: 2.6→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12803 0 0 24 12827
Biso mean---66.96 -
Num. residues----1651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01913072
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212572
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.97517736
X-RAY DIFFRACTIONr_angle_other_deg1.144329100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90751641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3924.564550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.757152177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6451560
X-RAY DIFFRACTIONr_chiral_restr0.1420.22025
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02114520
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022636
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A98900.06
12B98900.06
21A100060.08
22C100060.08
31A100240.06
32D100240.06
41A99160.08
42E99160.08
51A98480.07
52F98480.07
61A100660.07
62G100660.07
71A101800.08
72H101800.08
81A98640.08
82I98640.08
91A98320.07
92J98320.07
101B97720.07
102C97720.07
111B100060.06
112D100060.06
121B98360.06
122E98360.06
131B97900.07
132F97900.07
141B99180.06
142G99180.06
151B99740.06
152H99740.06
161B97720.06
162I97720.06
171B97800.07
172J97800.07
181C98820.07
182D98820.07
191C98760.07
192E98760.07
201C97980.08
202F97980.08
211C99880.07
212G99880.07
221C100360.08
222H100360.08
231C97680.07
232I97680.07
241C97960.08
242J97960.08
251D99200.06
252E99200.06
261D99100.07
262F99100.07
271D99740.05
272G99740.05
281D100400.06
282H100400.06
291D99120.06
292I99120.06
301D98780.06
302J98780.06
311E97920.07
312F97920.07
321E99060.07
322G99060.07
331E99520.07
332H99520.07
341E97900.08
342I97900.08
351E98820.08
352J98820.08
361F98200.07
362G98200.07
371F99240.07
372H99240.07
381F97680.07
382I97680.07
391F97340.07
392J97340.07
401G101640.06
402H101640.06
411G98260.06
412I98260.06
421G98360.07
422J98360.07
431H99220.07
432I99220.07
441H99100.08
442J99100.08
451I97480.08
452J97480.08
LS refinement shellResolution: 2.602→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 192 -
Rwork0.313 4072 -
all-4264 -
obs--89.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.22010.4119-0.05341.15540.10851.4938-0.08990.0275-0.0448-0.04190.0396-0.1235-0.09820.15130.05030.08850.01330.02880.1801-0.01110.0326.51530.2592-61.5739
20.7447-0.20580.20560.8034-0.37272.4291-0.00630.037-0.01560.0076-0.03380.015-0.13280.11690.04010.1007-0.00690.03570.1376-0.01070.018218.991246.3283-40.4672
31.00970.03690.31590.685-0.13521.4738-0.0048-0.0515-0.03940.0802-0.0398-0.1434-0.09480.12160.04450.0729-0.01640.00370.15910.02080.040225.172532.5301-10.6438
40.99620.2237-0.55271.3652-0.11310.9090.0196-0.05930.05880.1328-0.0688-0.0653-0.09360.01770.04920.0696-0.0061-0.0050.1055-0.00570.02312.415626.02652.8546
50.53590.61530.25391.5123-0.06821.11430.0286-0.1448-0.1250.1225-0.0353-0.10030.0424-0.12930.00680.0581-0.00940.01130.11860.02480.0443-1.8038-6.95046.4423
60.99890.11810.00320.34060.14391.49710.0547-0.08040.02880.0997-0.03190.03390.0874-0.0697-0.02270.1076-0.01280.01270.1938-0.02490.0322-24.5491-15.7829-6.4132
70.20.33260.0740.56060.0841.18350.02660.0124-0.00560.0314-0.0101-0.00450.17260.0031-0.01650.14150.03670.00570.1980.00190.0211-18.8047-32.6048-34.7604
80.89050.26490.31461.00370.00131.881-0.031-00.0087-0.05620.0120.02740.0573-0.09940.0190.11030.0154-0.0150.17410.01810.0056-27.1607-18.8616-56.9924
90.93910.4443-0.64561.00030.24951.1838-0.05970.1245-0.0933-0.1132-0.0049-0.04650.05150.05360.06460.19590.0028-0.0040.1960.02350.0245-2.1374-9.2122-76.4666
100.71730.40020.14391.295-0.18651.53540.00370.18780.0705-0.15330.06250.04640.0216-0.0938-0.06610.14560.0005-0.00180.17410.01170.01320.416618.2124-77.9616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION2B1 - 165
3X-RAY DIFFRACTION3C1 - 166
4X-RAY DIFFRACTION4D1 - 165
5X-RAY DIFFRACTION5E2 - 165
6X-RAY DIFFRACTION6F2 - 165
7X-RAY DIFFRACTION7G2 - 165
8X-RAY DIFFRACTION8H2 - 166
9X-RAY DIFFRACTION9I2 - 164
10X-RAY DIFFRACTION10J2 - 165

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more