[English] 日本語
Yorodumi
- PDB-5b8b: Crystal structure of reduced chimeric E.coli AhpC1-186-YFSKHN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b8b
TitleCrystal structure of reduced chimeric E.coli AhpC1-186-YFSKHN
ComponentsAlkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
KeywordsOXIDOREDUCTASE / Alkylhydroperoxide reductase / AhpC / Peroxiredoxins / chimeric
Function / homology
Function and homology information


response to alkyl hydroperoxide / respiratory burst involved in inflammatory response / alkyl hydroperoxide reductase complex / peptidyl-histidine phosphorylation / hydroperoxide reductase activity / cellular response to sulfate starvation / NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / leukocyte activation / negative regulation of T cell differentiation ...response to alkyl hydroperoxide / respiratory burst involved in inflammatory response / alkyl hydroperoxide reductase complex / peptidyl-histidine phosphorylation / hydroperoxide reductase activity / cellular response to sulfate starvation / NADH-dependent peroxiredoxin / NADH-dependent peroxiredoxin activity / leukocyte activation / negative regulation of T cell differentiation / siderophore biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / response to hydroperoxide / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / T cell homeostasis / antioxidant activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of blood coagulation / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / thymus development / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to oxidative stress / regulation of apoptotic process / response to oxidative stress / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / identical protein binding / membrane / cytoplasm / 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 / 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 / Peroxiredoxin-2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKamariah, N. / Sek, M.F. / Eisenhaber, B. / Eisenhaber, F. / Gruber, G.
Citation
Journal: Sci Rep / Year: 2016
Title: Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins.
Authors: Kamariah, N. / Sek, M.F. / Eisenhaber, B. / Eisenhaber, F. / Gruber, G.
#1: Journal: Acta Cryst D / Year: 2014
Title: The ups and downs in AhpF: Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli
Authors: Dip, P.V. / Kamariah, N. / Manimekalai, M.S.S. / Nartey, W. / Balakrishna, A.M. / Eisenhaber, F. / Eisenhaber, B. / Gruber, G.
History
DepositionJun 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
B: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
I: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
J: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
C: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
D: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
F: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
E: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
G: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
H: Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,86624
Polymers214,52110
Non-polymers1,34514
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.494, 135.654, 106.489
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 160 / Label seq-ID: 1 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CE
4DF
5EH
6FG
7GI
8HJ
9IC
10JD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.407122, -0.866027, -0.290256), (-0.864603, -0.46786, 0.183221), (-0.294473, 0.176363, -0.939245)122.61417, 190.8903, 25.52711
3given(0.421763, 0.544724, 0.724839), (0.038971, 0.787791, -0.614709), (-0.905868, 0.287509, 0.311033)-75.82171, 40.78556, -5.68726
4given(0.436168, -0.581192, 0.687003), (-0.583011, -0.764062, -0.276238), (0.68546, -0.280044, -0.672101)64.23018, 234.28349, 64.16537
5given(0.484793, 0.045585, -0.87344), (0.47045, 0.828282, 0.304346), (0.737328, -0.558455, 0.3801)20.91525, 9.6996, 74.60953
6given(-0.466715, -0.517387, -0.717278), (-0.469069, -0.542748, 0.696706), (-0.749768, 0.661616, 0.010619)99.51662, 183.14513, -48.2071
7given(-0.999161, -0.030495, 0.027333), (0.040522, -0.832644, 0.552324), (0.005915, 0.552969, 0.833181)31.09749, 215.11931, -63.90782
8given(-0.459341, 0.525082, -0.716446), (0.830765, 0.539427, -0.13729), (0.314382, -0.658261, -0.684)-29.69081, 48.34546, 114.954
9given(-0.441422, 0.858267, 0.261772), (0.563009, 0.492082, -0.663985), (-0.69869, -0.145718, -0.700428)-91.80576, 70.97549, 66.38319
10given(-0.438604, -0.044551, 0.897575), (-0.005183, -0.998628, -0.052099), (0.898665, -0.027503, 0.437772)5.68661, 249.37231, 4.02761

-
Components

#1: Protein
Alkyl hydroperoxide reductase subunit C,Peroxiredoxin-2 / Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / SCRP-23 / Sulfate starvation-induced ...Alkyl hydroperoxide reductase protein C22 / Peroxiredoxin / SCRP-23 / Sulfate starvation-induced protein 8 / SSI8 / Thioredoxin peroxidase


Mass: 21452.109 Da / Num. of mol.: 10 / Fragment: UNP RESIDUES 1-186,UNP RESIDUES 193-198
Source method: isolated from a genetically manipulated source
Details: The fusion protein of E.coli AhpC (residues 1-186) and human Prx2 (residues 193-198)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: ahpC, b0605, JW0598, PRDX2, NKEFB, TDPX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE08, UniProt: P32119, peroxiredoxin
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 100 mM MES pH 6.5, 5% Dioxane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 44808 / % possible obs: 92.9 % / Redundancy: 3.1 % / Net I/σ(I): 8.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.9 % / % possible all: 92

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8J

1n8j


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.847 / SU B: 61.738 / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28366 2147 5 %RANDOM
Rwork0.24858 ---
obs0.25033 40616 88.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.836 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å22.24 Å2
2---0.99 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13005 0 70 19 13094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212343
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9418097
X-RAY DIFFRACTIONr_angle_other_deg0.816328470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.57851639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48424.59647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.149152205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4091560
X-RAY DIFFRACTIONr_chiral_restr0.0540.21990
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023089
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3945.2136586
X-RAY DIFFRACTIONr_mcbond_other0.3945.2136585
X-RAY DIFFRACTIONr_mcangle_it0.7227.8178215
X-RAY DIFFRACTIONr_mcangle_other0.7227.8178216
X-RAY DIFFRACTIONr_scbond_it0.255.2796771
X-RAY DIFFRACTIONr_scbond_other0.245.2226716
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4667.8269799
X-RAY DIFFRACTIONr_long_range_B_refined2.76940.50814067
X-RAY DIFFRACTIONr_long_range_B_other2.76840.50914068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2468 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.570.5
Bmedium positional0.410.5
Cmedium positional0.440.5
Dmedium positional0.480.5
Emedium positional0.390.5
Fmedium positional0.380.5
Gmedium positional0.440.5
Hmedium positional0.360.5
Imedium positional0.370.5
Jmedium positional0.390.5
Amedium thermal2.372
Bmedium thermal2.792
Cmedium thermal2.932
Dmedium thermal2.512
Emedium thermal2.052
Fmedium thermal3.052
Gmedium thermal2.952
Hmedium thermal3.22
Imedium thermal3.342
Jmedium thermal1.892
LS refinement shellResolution: 3.102→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 101 -
Rwork0.338 2076 -
obs--61.31 %
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)
12.94670.6183-2.14131.1113-0.39554.4033-0.00250.0110.4411-0.0950.2028-0.29780.17910.1187-0.20030.2641-0.0785-0.22290.12020.04550.554854.8718111.431823.7343
22.197-0.95272.07424.1041-0.07134.15730.359-0.0193-0.14830.2556-0.3799-0.58150.210.27930.02090.2834-0.0581-0.17760.21060.10840.282441.526495.59916.4987
35.8665-1.4558-1.09122.00941.06733.5394-0.0672-0.6890.3105-0.07990.2219-0.6242-0.22260.3745-0.15470.4571-0.0338-0.25620.2258-0.10770.432427.232113.835-17.843
45.2384-1.0621-2.11982.93871.16284.4844-0.0205-0.65150.14840.30180.0701-0.08710.09440.3906-0.04960.33160.0383-0.31120.24560.01890.37580.313109.823-17.252
54.0356-0.9175-0.03593.405-0.82123.75930.03730.39770.0408-0.2818-0.2752-0.00190.16120.16850.23790.1886-0.0059-0.08620.07620.05110.0999-15.146138.387-6.996
64.218-1.6401-0.49015.07280.73880.944-0.05880.2489-0.0359-0.2691-0.10230.1283-0.0667-0.13290.16110.27280.0244-0.15210.037-0.03630.106-27.464134.38416.788
72.2723-0.0528-0.41952.26681.99756.2201-0.0474-0.0742-0.0384-0.0169-0.02210.2429-0.0681-0.54520.06950.112-0.0138-0.08430.14920.13650.2336-12.62151.91141.026
82.1777-1.8531-0.54866.07111.6372.72680.2060.1829-0.07540.089-0.12740.2063-0.0204-0.0954-0.07850.1762-0.0088-0.11230.02280.02150.1103-3.021135.07260.095
92.92720.65131.85173.05660.74022.931-0.0073-0.51130.15170.4437-0.1318-0.2172-0.3461-0.25840.13910.5236-0.0457-0.24730.18070.07230.206130.556135.44560.752
106.23970.64850.94382.4989-0.12083.0232-0.3637-0.33140.39720.12580.26350.1038-0.2108-0.1870.10020.41730.0458-0.16850.13080.04230.131139.965110.62354.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION2B1 - 162
3X-RAY DIFFRACTION3C1 - 162
4X-RAY DIFFRACTION4D1 - 164
5X-RAY DIFFRACTION5E1 - 165
6X-RAY DIFFRACTION6F1 - 163
7X-RAY DIFFRACTION7G1 - 162
8X-RAY DIFFRACTION8H1 - 165
9X-RAY DIFFRACTION9I1 - 161
10X-RAY DIFFRACTION10J1 - 166

+
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://pdbjlvh1.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