[English] 日本語
Yorodumi
- PDB-1zye: Crystal structure analysis of Bovine Mitochondrial Peroxiredoxin III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zye
TitleCrystal structure analysis of Bovine Mitochondrial Peroxiredoxin III
ComponentsThioredoxin-dependent peroxide reductase
KeywordsOXIDOREDUCTASE / catenane / dodecamer / peroxiredoxin
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis / cellular response to reactive oxygen species / regulation of mitochondrial membrane potential / hydrogen peroxide catabolic process ...Detoxification of Reactive Oxygen Species / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cell redox homeostasis / cellular response to reactive oxygen species / regulation of mitochondrial membrane potential / hydrogen peroxide catabolic process / mitochondrion organization / response to hydrogen peroxide / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...: / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-dependent peroxide reductase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCao, Z. / Roszak, A.W. / Gourlay, L.J. / Lindsay, J.G. / Isaacs, N.W.
CitationJournal: Structure / Year: 2005
Title: Bovine Mitochondrial Peroxiredoxin III Forms a Two-Ring Catenane
Authors: Cao, Z. / Roszak, A.W. / Gourlay, L.J. / Lindsay, J.G. / Isaacs, N.W.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 9, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin-dependent peroxide reductase
B: Thioredoxin-dependent peroxide reductase
C: Thioredoxin-dependent peroxide reductase
D: Thioredoxin-dependent peroxide reductase
E: Thioredoxin-dependent peroxide reductase
F: Thioredoxin-dependent peroxide reductase
G: Thioredoxin-dependent peroxide reductase
H: Thioredoxin-dependent peroxide reductase
I: Thioredoxin-dependent peroxide reductase
J: Thioredoxin-dependent peroxide reductase
K: Thioredoxin-dependent peroxide reductase
L: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)292,39912
Polymers292,39912
Non-polymers00
Water1629
1
A: Thioredoxin-dependent peroxide reductase
B: Thioredoxin-dependent peroxide reductase
C: Thioredoxin-dependent peroxide reductase
D: Thioredoxin-dependent peroxide reductase
E: Thioredoxin-dependent peroxide reductase
F: Thioredoxin-dependent peroxide reductase
G: Thioredoxin-dependent peroxide reductase
H: Thioredoxin-dependent peroxide reductase
I: Thioredoxin-dependent peroxide reductase
J: Thioredoxin-dependent peroxide reductase
K: Thioredoxin-dependent peroxide reductase
L: Thioredoxin-dependent peroxide reductase

A: Thioredoxin-dependent peroxide reductase
B: Thioredoxin-dependent peroxide reductase
C: Thioredoxin-dependent peroxide reductase
D: Thioredoxin-dependent peroxide reductase
E: Thioredoxin-dependent peroxide reductase
F: Thioredoxin-dependent peroxide reductase
G: Thioredoxin-dependent peroxide reductase
H: Thioredoxin-dependent peroxide reductase
I: Thioredoxin-dependent peroxide reductase
J: Thioredoxin-dependent peroxide reductase
K: Thioredoxin-dependent peroxide reductase
L: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)584,79824
Polymers584,79824
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18040 Å2
ΔGint-121 kcal/mol
Surface area73740 Å2
MethodPISA
3
A: Thioredoxin-dependent peroxide reductase
B: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: Thioredoxin-dependent peroxide reductase
D: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Thioredoxin-dependent peroxide reductase
F: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
G: Thioredoxin-dependent peroxide reductase
H: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
I: Thioredoxin-dependent peroxide reductase
J: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
K: Thioredoxin-dependent peroxide reductase
L: Thioredoxin-dependent peroxide reductase


Theoretical massNumber of molelcules
Total (without water)48,7332
Polymers48,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)300.995, 80.679, 124.295
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31B
41A
51B
61A
12C
22A
13D
23A
33D
43A
14E
24A
34E
44A
54E
64A
74E
84A
94E
104A
15F
25A
35F
45A
55F
65A
75F
85A
95F
105A
16G
26A
36G
46A
56G
66A
76G
86A
96G
106A
116G
126A
136G
146A
17H
27A
37H
47A
57H
67A
77H
87A
97H
107A
117H
127A
137H
147A
157H
167A
18I
28A
38I
48A
58I
68A
78I
88A
19J
29A
39J
49A
59J
69A
110K
210A
310K
410A
510K
610A
111L
211A
311L
411A
511L
611A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLYGLY1BB2 - 1927 - 44
211PROPROGLYGLY1AA2 - 1927 - 44
321GLUGLUGLUGLU3BB2045
421GLUGLUGLUGLU3AA2045
531PHEPHEALAALA1BB21 - 16346 - 188
631PHEPHEALAALA1AA21 - 16346 - 188
112PROPROALAALA1CC2 - 16327 - 188
212PROPROALAALA1AA2 - 16327 - 188
113PROPROVALVAL1DD2 - 16127 - 186
213PROPROVALVAL1AA2 - 16127 - 186
323GLUGLUALAALA3DD162 - 163187 - 188
423GLUGLUALAALA3AA162 - 163187 - 188
114PROPROLYSLYS1EE2 - 10527 - 130
214PROPROLYSLYS1AA2 - 10527 - 130
324GLNGLNGLNGLN3EE106131
424GLNGLNGLNGLN3AA106131
534ILEILESERSER1EE107 - 108132 - 133
634ILEILESERSER1AA107 - 108132 - 133
744ARGARGARGARG3EE109134
844ARGARGARGARG3AA109134
954ASPASPALAALA1EE110 - 163135 - 188
1054ASPASPALAALA1AA110 - 163135 - 188
115PROPROLEULEU1FF2 - 10327 - 128
215PROPROLEULEU1AA2 - 10327 - 128
325THRTHRTHRTHR3FF104129
425THRTHRTHRTHR3AA104129
535LYSLYSLYSLYS1FF105130
635LYSLYSLYSLYS1AA105130
745GLNGLNGLNGLN3FF106131
845GLNGLNGLNGLN3AA106131
955ILEILEALAALA1FF107 - 163132 - 188
1055ILEILEALAALA1AA107 - 163132 - 188
116PROPROLEULEU1GG2 - 10327 - 128
216PROPROLEULEU1AA2 - 10327 - 128
326THRTHRTHRTHR3GG104129
426THRTHRTHRTHR3AA104129
536LYSLYSLYSLYS1GG105130
636LYSLYSLYSLYS1AA105130
746GLNGLNGLNGLN3GG106131
846GLNGLNGLNGLN3AA106131
956ILEILEGLNGLN1GG107 - 159132 - 184
1056ILEILEGLNGLN1AA107 - 159132 - 184
1166PHEPHEPHEPHE3GG160185
1266PHEPHEPHEPHE3AA160185
1376VALVALALAALA1GG161 - 163186 - 188
1476VALVALALAALA1AA161 - 163186 - 188
117PROPROASPASP1HH2 - 6327 - 88
217PROPROASPASP1AA2 - 6327 - 88
327GLNGLNGLNGLN3HH106131
427GLNGLNGLNGLN3AA106131
537ILEILESERSER1HH107 - 108132 - 133
637ILEILESERSER1AA107 - 108132 - 133
747ALAALAALAALA3HH163188
847ALAALAALAALA3AA163188
957VALVALVALVAL3HH6489
1057VALVALVALVAL3AA6489
1167ASNASNLYSLYS1HH65 - 10590 - 130
1267ASNASNLYSLYS1AA65 - 10590 - 130
1377ARGARGARGARG3HH109134
1477ARGARGARGARG3AA109134
1587ASPASPGLUGLU1HH110 - 162135 - 187
1687ASPASPGLUGLU1AA110 - 162135 - 187
118PROPROVALVAL1II2 - 6427 - 89
218PROPROVALVAL1AA2 - 6427 - 89
328ASNASNASNASN3II6590
428ASNASNASNASN3AA6590
538CYSCYSVALVAL1II66 - 16191 - 186
638CYSCYSVALVAL1AA66 - 16191 - 186
748GLUGLUALAALA3II162 - 163187 - 188
848GLUGLUALAALA3AA162 - 163187 - 188
119PROPROHISHIS1JJ2 - 6227 - 87
219PROPROHISHIS1AA2 - 6227 - 87
329ASPASPASPASP3JJ6388
429ASPASPASPASP3AA6388
539VALVALALAALA1JJ64 - 16389 - 188
639VALVALALAALA1AA64 - 16389 - 188
1110PROPROGLYGLY1KK2 - 1927 - 44
2110PROPROGLYGLY1AA2 - 1927 - 44
3210GLUGLUGLUGLU3KK2045
4210GLUGLUGLUGLU3AA2045
5310PHEPHEALAALA1KK21 - 16346 - 188
6310PHEPHEALAALA1AA21 - 16346 - 188
1111PROPROPHEPHE1LL2 - 6127 - 86
2111PROPROPHEPHE1AA2 - 6127 - 86
3211HISHISHISHIS3LL6287
4211HISHISHISHIS3AA6287
5311ASPASPALAALA1LL63 - 16388 - 188
6311ASPASPALAALA1AA63 - 16388 - 188

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

-
Components

#1: Protein
Thioredoxin-dependent peroxide reductase / Peroxiredoxin 3 / Antioxidant protein 1 / AOP-1 / SP-22 protein / Mitochondrial Peroxiredoxin III


Mass: 24366.580 Da / Num. of mol.: 12 / Mutation: C168S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: pET-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P35705, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: ammonium sulfate, isopropanol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→35 Å / Num. all: 41825 / Num. obs: 41825 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 80.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.1
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.3 / Num. unique all: 6070 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1qmv

1qmv


Resolution: 3.3→35 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.883 / SU B: 24.9 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.55 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26486 2109 5 %RANDOM
Rwork0.22624 ---
all0.22819 41825 --
obs0.22819 39668 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-2.14 Å2
2---1.53 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 3.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15192 0 0 9 15201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02215576
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.95421144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79151932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.035684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.253152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7971560
X-RAY DIFFRACTIONr_chiral_restr0.0930.22412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211736
X-RAY DIFFRACTIONr_nbd_refined0.2350.27120
X-RAY DIFFRACTIONr_nbtor_refined0.320.210656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2469
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3620.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.24
X-RAY DIFFRACTIONr_mcbond_it0.6151.59812
X-RAY DIFFRACTIONr_mcangle_it1.138215624
X-RAY DIFFRACTIONr_scbond_it1.34236342
X-RAY DIFFRACTIONr_scangle_it2.474.55520
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1261tight positional0.050.05
2C1266tight positional0.050.05
3D1260tight positional0.070.05
4E1254tight positional0.060.05
5F1258tight positional0.060.05
6G1251tight positional0.050.05
7H1250tight positional0.060.05
8I1256tight positional0.060.05
9J1262tight positional0.060.05
10K1261tight positional0.050.05
11L1260tight positional0.050.05
1B5loose positional0.985
3D6loose positional1.415
4E12loose positional1.555
5F8loose positional0.675
6G15loose positional0.815
7H16loose positional1.295
8I10loose positional1.395
9J4loose positional0.275
10K5loose positional0.485
11L6loose positional0.525
1B1261tight thermal0.120.5
2C1266tight thermal0.110.5
3D1260tight thermal0.150.5
4E1254tight thermal0.110.5
5F1258tight thermal0.150.5
6G1251tight thermal0.120.5
7H1250tight thermal0.10.5
8I1256tight thermal0.10.5
9J1262tight thermal0.120.5
10K1261tight thermal0.10.5
11L1260tight thermal0.170.5
1B5loose thermal3.3610
3D6loose thermal1.0910
4E12loose thermal5.9710
5F8loose thermal0.7710
6G15loose thermal1.1810
7H16loose thermal4.3610
8I10loose thermal1.8210
9J4loose thermal1.810
10K5loose thermal2.810
11L6loose thermal7.5810
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 160 -
Rwork0.305 2911 -
obs-2911 100 %

+
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