[English] 日本語
Yorodumi
- PDB-3zlp: Crystal structure of Schistosoma mansoni Peroxiredoxin 1 C48P mut... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zlp
TitleCrystal structure of Schistosoma mansoni Peroxiredoxin 1 C48P mutant form with four decamers in the asymmetric unit
ComponentsTHIOREDOXIN PEROXIDASE
KeywordsOXIDOREDUCTASE / PEROXIDASE / SCHISTOSOMIASIS / CHAPERONE / THIOREDOXIN FOLD
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / identical protein binding
Similarity search - Function
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 ...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
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.515 Å
AuthorsSaccoccia, F. / Angelucci, F. / Ardini, M. / Boumis, G. / Brunori, M. / DiLeandro, L. / Ippoliti, R. / Miele, A.E. / Natoli, G. / Scotti, S. / Bellelli, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Switching between the Alternative Structures and Functions of a 2-Cys Peroxiredoxin, by Site-Directed Mutagenesis
Authors: Angelucci, F. / Saccoccia, F. / Ardini, M. / Boumis, G. / Brunori, M. / Dileandro, L. / Ippoliti, R. / Miele, A.E. / Natoli, G. / Scotti, S. / Bellelli, A.
History
DepositionFeb 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN PEROXIDASE
B: THIOREDOXIN PEROXIDASE
C: THIOREDOXIN PEROXIDASE
D: THIOREDOXIN PEROXIDASE
E: THIOREDOXIN PEROXIDASE
F: THIOREDOXIN PEROXIDASE
G: THIOREDOXIN PEROXIDASE
H: THIOREDOXIN PEROXIDASE
I: THIOREDOXIN PEROXIDASE
J: THIOREDOXIN PEROXIDASE
K: THIOREDOXIN PEROXIDASE
L: THIOREDOXIN PEROXIDASE
M: THIOREDOXIN PEROXIDASE
N: THIOREDOXIN PEROXIDASE
O: THIOREDOXIN PEROXIDASE
P: THIOREDOXIN PEROXIDASE
Q: THIOREDOXIN PEROXIDASE
R: THIOREDOXIN PEROXIDASE
S: THIOREDOXIN PEROXIDASE
T: THIOREDOXIN PEROXIDASE
U: THIOREDOXIN PEROXIDASE
V: THIOREDOXIN PEROXIDASE
W: THIOREDOXIN PEROXIDASE
X: THIOREDOXIN PEROXIDASE
Y: THIOREDOXIN PEROXIDASE
Z: THIOREDOXIN PEROXIDASE
a: THIOREDOXIN PEROXIDASE
b: THIOREDOXIN PEROXIDASE
c: THIOREDOXIN PEROXIDASE
d: THIOREDOXIN PEROXIDASE
e: THIOREDOXIN PEROXIDASE
f: THIOREDOXIN PEROXIDASE
g: THIOREDOXIN PEROXIDASE
h: THIOREDOXIN PEROXIDASE
i: THIOREDOXIN PEROXIDASE
j: THIOREDOXIN PEROXIDASE
k: THIOREDOXIN PEROXIDASE
l: THIOREDOXIN PEROXIDASE
m: THIOREDOXIN PEROXIDASE
n: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)846,60340
Polymers846,60340
Non-polymers00
Water0
1
A: THIOREDOXIN PEROXIDASE
B: THIOREDOXIN PEROXIDASE
C: THIOREDOXIN PEROXIDASE
D: THIOREDOXIN PEROXIDASE
E: THIOREDOXIN PEROXIDASE
F: THIOREDOXIN PEROXIDASE
G: THIOREDOXIN PEROXIDASE
H: THIOREDOXIN PEROXIDASE
I: THIOREDOXIN PEROXIDASE
J: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)211,65110
Polymers211,65110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20810 Å2
ΔGint-180.6 kcal/mol
Surface area80680 Å2
MethodPISA
2
K: THIOREDOXIN PEROXIDASE
L: THIOREDOXIN PEROXIDASE
M: THIOREDOXIN PEROXIDASE
N: THIOREDOXIN PEROXIDASE
O: THIOREDOXIN PEROXIDASE
P: THIOREDOXIN PEROXIDASE
Q: THIOREDOXIN PEROXIDASE
R: THIOREDOXIN PEROXIDASE
S: THIOREDOXIN PEROXIDASE
T: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)211,65110
Polymers211,65110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22200 Å2
ΔGint-103.1 kcal/mol
Surface area81620 Å2
MethodPISA
3
U: THIOREDOXIN PEROXIDASE
V: THIOREDOXIN PEROXIDASE
W: THIOREDOXIN PEROXIDASE
X: THIOREDOXIN PEROXIDASE
Y: THIOREDOXIN PEROXIDASE
Z: THIOREDOXIN PEROXIDASE
a: THIOREDOXIN PEROXIDASE
b: THIOREDOXIN PEROXIDASE
c: THIOREDOXIN PEROXIDASE
d: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)211,65110
Polymers211,65110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21400 Å2
ΔGint-136.9 kcal/mol
Surface area81280 Å2
MethodPISA
4
e: THIOREDOXIN PEROXIDASE
f: THIOREDOXIN PEROXIDASE
g: THIOREDOXIN PEROXIDASE
h: THIOREDOXIN PEROXIDASE
i: THIOREDOXIN PEROXIDASE
j: THIOREDOXIN PEROXIDASE
k: THIOREDOXIN PEROXIDASE
l: THIOREDOXIN PEROXIDASE
m: THIOREDOXIN PEROXIDASE
n: THIOREDOXIN PEROXIDASE


Theoretical massNumber of molelcules
Total (without water)211,65110
Polymers211,65110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15540 Å2
ΔGint-60.7 kcal/mol
Surface area81190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.179, 190.300, 211.995
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ...
THIOREDOXIN PEROXIDASE / PEROXIREDOXIN I / THIOREDOXIN PEROXIDASE 1


Mass: 21165.084 Da / Num. of mol.: 40 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O97161, peroxiredoxin

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.97 %
Description: HIGHEST RESOLUTION SHELL CHOSEN ON THE BASIS OF CCHALF VALUE. FOR THE HIGHEST RESOLUTION SHELL REPORTED HERE, CCHALF WAS 0.88
Crystal growDetails: 100 MM BIS-TRIS PROPANE, 200 MM NABR, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3.52→48.76 Å / Num. obs: 91789 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 75.6 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 5.75
Reflection shellResolution: 3.51→3.72 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 0.84 / % possible all: 90.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZTL

3ztl


Resolution: 3.515→48.758 Å / σ(F): 1.34 / Phase error: 32.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2893 4669 5.1 %
Rwork0.2767 --
obs0.276 92082 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.01 Å2
Baniso -1Baniso -2Baniso -3
1-11.7615 Å20 Å2-1.8586 Å2
2--25.4292 Å20 Å2
3----41.6091 Å2
Refinement stepCycle: LAST / Resolution: 3.515→48.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52540 0 0 0 52540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553935
X-RAY DIFFRACTIONf_angle_d1.51272929
X-RAY DIFFRACTIONf_dihedral_angle_d17.06320192
X-RAY DIFFRACTIONf_chiral_restr0.0857789
X-RAY DIFFRACTIONf_plane_restr0.0079682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5161-3.57670.43111820.40693443X-RAY DIFFRACTION74
3.5767-3.64170.39142180.38154087X-RAY DIFFRACTION88
3.6417-3.71170.37562250.37194261X-RAY DIFFRACTION91
3.7117-3.78750.36742320.35024414X-RAY DIFFRACTION95
3.7875-3.86980.3652340.35214436X-RAY DIFFRACTION95
3.8698-3.95980.34552360.34334491X-RAY DIFFRACTION95
3.9598-4.05870.36942300.31164362X-RAY DIFFRACTION95
4.0587-4.16840.34242350.31044477X-RAY DIFFRACTION95
4.1684-4.2910.30162320.28964412X-RAY DIFFRACTION95
4.291-4.42940.29422330.28164427X-RAY DIFFRACTION95
4.4294-4.58760.28552340.27224446X-RAY DIFFRACTION95
4.5876-4.77110.28032350.26194456X-RAY DIFFRACTION95
4.7711-4.98810.27432340.26934450X-RAY DIFFRACTION95
4.9881-5.25080.31112330.26754430X-RAY DIFFRACTION95
5.2508-5.57930.29082370.27814486X-RAY DIFFRACTION95
5.5793-6.00940.30882340.30224446X-RAY DIFFRACTION95
6.0094-6.61280.27192340.26964449X-RAY DIFFRACTION95
6.6128-7.56660.29572340.25614460X-RAY DIFFRACTION95
7.5666-9.52150.212390.20264526X-RAY DIFFRACTION95
9.5215-48.70910.20322370.20054501X-RAY DIFFRACTION94

+
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