[English] 日本語
Yorodumi
- PDB-4xs4: Salmonella typhimurium AhpC C165S mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xs4
TitleSalmonella typhimurium AhpC C165S mutant
Components(Alkyl hydroperoxide reductase subunit C) x 2
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: 2.65 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 21, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2918
Polymers103,1745
Non-polymers1173
Water6,593366
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,58216
Polymers206,34710
Non-polymers2356
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area30160 Å2
ΔGint-185 kcal/mol
Surface area68120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.045, 172.100, 136.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

-
Components

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


Mass: 20625.123 Da / Num. of mol.: 4 / Mutation: C165S
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: Protein Alkyl hydroperoxide reductase subunit C / Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / Thioredoxin peroxidase


Mass: 20673.121 Da / Num. of mol.: 1 / Mutation: C165S
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
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Pretreatment with 2 mM mercaptoethanol, then crystallized in 1.4 M MgSO4, 0.1 M MES, 10 mM hydrogen peroxide, pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→72.7 Å / Num. obs: 43671 / % possible obs: 100 % / Redundancy: 12.1 % / Net I/σ(I): 6.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 0.9 / % possible all: 100

-
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: 2.65→68.105 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 4152 4.95 %imported from 4MA9
Rwork0.2015 ---
obs0.2036 83801 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→68.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 3 366 7503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147503
X-RAY DIFFRACTIONf_angle_d2.02410199
X-RAY DIFFRACTIONf_dihedral_angle_d14.9562705
X-RAY DIFFRACTIONf_chiral_restr0.0991121
X-RAY DIFFRACTIONf_plane_restr0.0111335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.68010.31371390.30832677X-RAY DIFFRACTION100
2.6801-2.71170.33861400.31332652X-RAY DIFFRACTION100
2.7117-2.74470.33221490.31472697X-RAY DIFFRACTION100
2.7447-2.77950.34341330.31712609X-RAY DIFFRACTION100
2.7795-2.8160.29311730.29492663X-RAY DIFFRACTION100
2.816-2.85460.37961580.28722556X-RAY DIFFRACTION100
2.8546-2.89540.32281530.29332683X-RAY DIFFRACTION100
2.8954-2.93860.3661390.28122650X-RAY DIFFRACTION100
2.9386-2.98450.30851240.26582705X-RAY DIFFRACTION100
2.9845-3.03350.30261400.24922608X-RAY DIFFRACTION100
3.0335-3.08580.28821510.23492649X-RAY DIFFRACTION100
3.0858-3.14190.30021700.23622634X-RAY DIFFRACTION100
3.1419-3.20230.26231180.2382636X-RAY DIFFRACTION100
3.2023-3.26770.23741410.22452705X-RAY DIFFRACTION100
3.2677-3.33870.26481350.20392661X-RAY DIFFRACTION100
3.3387-3.41640.29321240.18932618X-RAY DIFFRACTION100
3.4164-3.50180.2891170.19642673X-RAY DIFFRACTION100
3.5018-3.59650.23471120.21872705X-RAY DIFFRACTION100
3.5965-3.70230.4751110.31742663X-RAY DIFFRACTION100
3.7023-3.82180.27081080.22252678X-RAY DIFFRACTION100
3.8218-3.95840.18391590.16662677X-RAY DIFFRACTION100
3.9584-4.11690.22351570.1682624X-RAY DIFFRACTION100
4.1169-4.30420.19071640.1382624X-RAY DIFFRACTION100
4.3042-4.53110.18181260.1252657X-RAY DIFFRACTION100
4.5311-4.81490.12241010.11652689X-RAY DIFFRACTION100
4.8149-5.18660.15731380.13082632X-RAY DIFFRACTION100
5.1866-5.70830.1851370.15062664X-RAY DIFFRACTION100
5.7083-6.53370.20731620.172623X-RAY DIFFRACTION100
6.5337-8.22950.19681250.17762694X-RAY DIFFRACTION100
8.2295-68.12750.19181480.17642643X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
13.1070.5082-0.34212.8813-1.74664.1259-0.0264-0.0066-0.0194-0.05360.33730.32730.0374-0.6158-0.29090.2754-0.0184-0.04050.26650.07390.2725-14.68659.8539122.3648
23.35430.7254-0.962.8714-0.24323.38250.07870.02750.14750.1650.12720.2334-0.2925-0.3069-0.14360.27330.0767-0.00560.2091-0.04490.2586-2.894831.276126.9524
34.6504-1.03970.96481.6816-0.76631.20560.1830.68520.2149-0.1541-0.1083-0.3387-0.22970.5735-0.08410.4046-0.09340.02290.5302-0.13670.315531.156232.0825108.2725
43.6437-1.0813-0.41523.9242-0.23762.17640.00160.3615-0.041-0.0665-0.1729-0.2875-0.1825-0.01680.15540.314-0.1571-0.05210.4278-0.11690.365247.181336.2963124.5348
53.1027-0.5626-0.23714.3861-2.68373.83640.19510.0390.0596-0.4266-0.5025-1.09170.61440.75590.28830.47540.06270.07620.6096-0.03230.683169.46693.2207125.2767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

+
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