[English] 日本語
Yorodumi
- PDB-3tjf: Crystal Structure of human peroxiredoxin IV C51A mutant in reduce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tjf
TitleCrystal Structure of human peroxiredoxin IV C51A mutant in reduced form
ComponentsPeroxiredoxin-4
KeywordsOXIDOREDUCTASE / thioredoxin fold / sulfenylation / endoplasmic reticulum
Function / homology
Function and homology information


negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / : / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development ...negative regulation of male germ cell proliferation / I-kappaB phosphorylation / thioredoxin-dependent peroxiredoxin / molecular sequestering activity / thioredoxin peroxidase activity / : / extracellular matrix organization / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / secretory granule lumen / spermatogenesis / molecular adaptor activity / response to oxidative stress / ficolin-1-rich granule lumen / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding / nucleus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Reduced and of Oxidized Peroxiredoxin IV Enzyme Reveals a Stable Oxidized Decamer and a Non-disulfide-bonded Intermediate in the Catalytic Cycle.
Authors: Cao, Z. / Tavender, T.J. / Roszak, A.W. / Cogdell, R.J. / Bulleid, N.J.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,45820
Polymers144,0175
Non-polymers1,44115
Water14,304794
1
A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules

A: Peroxiredoxin-4
B: Peroxiredoxin-4
C: Peroxiredoxin-4
D: Peroxiredoxin-4
E: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,91640
Polymers288,03410
Non-polymers2,88230
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area36110 Å2
ΔGint-648 kcal/mol
Surface area71050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.348, 138.849, 96.236
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Peroxiredoxin-4 / Peroxiredoxin IV / Antioxidant enzyme AOE372 / AOE37-2 / Prx-IV / Thioredoxin peroxidase AO372 / ...Peroxiredoxin IV / Antioxidant enzyme AOE372 / AOE37-2 / Prx-IV / Thioredoxin peroxidase AO372 / Thioredoxin-dependent peroxide reductase A0372


Mass: 28803.428 Da / Num. of mol.: 5 / Fragment: UNP residues 38-271 / Mutation: C51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX4 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13162, peroxiredoxin
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.55 M ammonium sulfate, 12% glycerol, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2010 / Details: MIRRORS
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.04→28.97 Å / Num. all: 87136 / Num. obs: 87136 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.3
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6233 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0110refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PN8

2pn8


Resolution: 2.04→28.77 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.208 / SU ML: 0.098 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19711 4344 5 %RANDOM
Rwork0.15965 ---
all0.16152 87117 --
obs0.16152 82773 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.144 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å2-0.85 Å2
2---0.17 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7819 0 75 794 8688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228331
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.97611367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08951034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85323.955397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.202151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211550
X-RAY DIFFRACTIONr_chiral_restr0.1070.21227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216390
X-RAY DIFFRACTIONr_mcbond_it0.7691.54969
X-RAY DIFFRACTIONr_mcangle_it1.39328106
X-RAY DIFFRACTIONr_scbond_it2.24933362
X-RAY DIFFRACTIONr_scangle_it3.5464.53231
LS refinement shellResolution: 2.04→2.092 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 275 -
Rwork0.276 5926 -
obs-6233 96.29 %
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)
11.2639-0.29091.00710.9535-0.43811.9533-0.05170.07340.16490.0224-0.0166-0.0727-0.1610.11760.06840.0312-0.04080.00410.0678-0.00450.067316.21452.379412.2093
20.8589-0.39490.27681.817-0.35451.3976-0.0109-0.1356-0.00490.16950.00670.104-0.0363-0.10660.00430.0714-0.02660.01680.085-0.04040.03139.3411-6.929131.1809
30.2379-0.11560.13243.35720.21520.5831-0.0138-0.04550.03550.03730.0247-0.4007-0.01740.17-0.0110.03850.0067-0.00870.09860.01370.096528.4771-42.603633.0025
40.50940.33660.13651.64310.48971.4745-0.0076-0.09-0.02440.1722-0.03220.0648-0.0175-0.05950.03980.10890.04570.01760.11050.05460.03512.5346-57.811836.803
50.78140.1460.75780.76380.22212.40430.0060.0236-0.19960.00470.0287-0.0610.27610.1828-0.03470.06490.05260.03950.06250.00950.104410.7473-79.57893.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 269
2X-RAY DIFFRACTION2B75 - 269
3X-RAY DIFFRACTION3C74 - 269
4X-RAY DIFFRACTION4D75 - 268
5X-RAY DIFFRACTION5E73 - 268

+
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