[English] 日本語
Yorodumi
- PDB-4xts: Salmonella typhimurium AhpC T43A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xts
TitleSalmonella typhimurium AhpC T43A mutant
ComponentsAlkyl hydroperoxide reductase subunit C
KeywordsOXIDOREDUCTASE / peroxiredoxin / FF / PrxI / conformation
Function / homology
Function and homology information


NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
Similarity search - Function
Alkyl hydroperoxide reductase subunit C / 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 / Glutaredoxin ...Alkyl hydroperoxide reductase subunit C / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkyl hydroperoxide reductase C
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsPerkins, A. / Nelson, K. / Parsonage, D. / Poole, L. / Karplus, P.A.
CitationJournal: Antioxid.Redox Signal. / Year: 2018
Title: Experimentally Dissecting the Origins of Peroxiredoxin Catalysis.
Authors: Nelson, K.J. / Perkins, A. / Van Swearingen, A.E.D. / Hartman, S. / Brereton, A.E. / Parsonage, D. / Salsbury Jr., F.R. / Karplus, P.A. / Poole, L.B.
History
DepositionJan 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C
F: Alkyl hydroperoxide reductase subunit C
G: Alkyl hydroperoxide reductase subunit C
H: Alkyl hydroperoxide reductase subunit C
I: Alkyl hydroperoxide reductase subunit C
J: Alkyl hydroperoxide reductase subunit C
K: Alkyl hydroperoxide reductase subunit C
L: Alkyl hydroperoxide reductase subunit C
M: Alkyl hydroperoxide reductase subunit C
N: Alkyl hydroperoxide reductase subunit C
O: Alkyl hydroperoxide reductase subunit C
P: Alkyl hydroperoxide reductase subunit C
Q: Alkyl hydroperoxide reductase subunit C
R: Alkyl hydroperoxide reductase subunit C
S: Alkyl hydroperoxide reductase subunit C
T: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,18047
Polymers412,22320
Non-polymers95727
Water7,566420
1
A: Alkyl hydroperoxide reductase subunit C
B: Alkyl hydroperoxide reductase subunit C
C: Alkyl hydroperoxide reductase subunit C
D: Alkyl hydroperoxide reductase subunit C
E: Alkyl hydroperoxide reductase subunit C
F: Alkyl hydroperoxide reductase subunit C
G: Alkyl hydroperoxide reductase subunit C
H: Alkyl hydroperoxide reductase subunit C
I: Alkyl hydroperoxide reductase subunit C
J: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,60824
Polymers206,11210
Non-polymers49614
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18140 Å2
ΔGint-277 kcal/mol
Surface area64520 Å2
MethodPISA
2
K: Alkyl hydroperoxide reductase subunit C
L: Alkyl hydroperoxide reductase subunit C
M: Alkyl hydroperoxide reductase subunit C
N: Alkyl hydroperoxide reductase subunit C
O: Alkyl hydroperoxide reductase subunit C
P: Alkyl hydroperoxide reductase subunit C
Q: Alkyl hydroperoxide reductase subunit C
R: Alkyl hydroperoxide reductase subunit C
S: Alkyl hydroperoxide reductase subunit C
T: Alkyl hydroperoxide reductase subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,57323
Polymers206,11210
Non-polymers46113
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-261 kcal/mol
Surface area63990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.651, 109.454, 119.037
Angle α, β, γ (deg.)93.33, 110.02, 114.00
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Alkyl hydroperoxide reductase subunit C / Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / Thioredoxin peroxidase


Mass: 20611.162 Da / Num. of mol.: 20 / Mutation: T43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P0A251, peroxiredoxin
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 25% polyethylene glycol 3350, and 0.1 M BIS-TRIS pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→89.5 Å / Num. obs: 118972 / % possible obs: 96.3 % / Redundancy: 3.6 % / Net I/σ(I): 5.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA9

4ma9


Resolution: 2.704→63.511 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 11879 5 %imported from 4ma9
Rwork0.1899 ---
obs0.1927 237767 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.704→63.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25377 0 27 420 25824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01226026
X-RAY DIFFRACTIONf_angle_d1.65535271
X-RAY DIFFRACTIONf_dihedral_angle_d14.659322
X-RAY DIFFRACTIONf_chiral_restr0.0843860
X-RAY DIFFRACTIONf_plane_restr0.014605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7037-2.73450.37653270.31236000X-RAY DIFFRACTION76
2.7345-2.76660.35573520.31547350X-RAY DIFFRACTION93
2.7666-2.80040.41183860.31667296X-RAY DIFFRACTION93
2.8004-2.83580.33123700.29697418X-RAY DIFFRACTION94
2.8358-2.87310.34173900.2957269X-RAY DIFFRACTION93
2.8731-2.91250.36133680.30767416X-RAY DIFFRACTION94
2.9125-2.95410.36453810.30537501X-RAY DIFFRACTION94
2.9541-2.99820.37344220.28527339X-RAY DIFFRACTION95
2.9982-3.04510.34473920.27367609X-RAY DIFFRACTION95
3.0451-3.0950.32984300.26067365X-RAY DIFFRACTION95
3.095-3.14830.30164000.25547553X-RAY DIFFRACTION96
3.1483-3.20560.3063740.25527624X-RAY DIFFRACTION96
3.2056-3.26720.32144060.2547594X-RAY DIFFRACTION97
3.2672-3.33390.32244080.24777630X-RAY DIFFRACTION97
3.3339-3.40640.28594220.22767602X-RAY DIFFRACTION97
3.4064-3.48560.28514030.22127664X-RAY DIFFRACTION97
3.4856-3.57280.28024200.20427688X-RAY DIFFRACTION98
3.5728-3.66940.24264140.19867598X-RAY DIFFRACTION98
3.6694-3.77740.25073560.1957796X-RAY DIFFRACTION98
3.7774-3.89930.23694580.17727616X-RAY DIFFRACTION98
3.8993-4.03860.22033860.16337795X-RAY DIFFRACTION98
4.0386-4.20030.19744040.14717710X-RAY DIFFRACTION98
4.2003-4.39140.18264100.13337683X-RAY DIFFRACTION98
4.3914-4.62290.17864480.1247636X-RAY DIFFRACTION98
4.6229-4.91240.18024160.11727714X-RAY DIFFRACTION98
4.9124-5.29150.17324020.1247638X-RAY DIFFRACTION98
5.2915-5.82370.18554060.13237714X-RAY DIFFRACTION98
5.8237-6.66560.18063480.13977762X-RAY DIFFRACTION98
6.6656-8.39490.1663660.12387756X-RAY DIFFRACTION98
8.3949-63.52830.15774140.13317552X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 116.9394 Å / Origin y: 6.7638 Å / Origin z: 59.3817 Å
111213212223313233
T0.2539 Å20.0004 Å2-0.0156 Å2-0.2396 Å2-0.0082 Å2--0.2871 Å2
L0.1179 °2-0.0375 °20.0136 °2-0.0346 °2-0.0048 °2--0.0655 °2
S0.0191 Å °0.039 Å °0.0005 Å °-0.0081 Å °-0.0285 Å °0.0075 Å °0.0038 Å °0.0066 Å °0.0071 Å °
Refinement TLS groupSelection details: all

+
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