[English] 日本語
Yorodumi
- PDB-2i81: Crystal Structure of Plasmodium vivax 2-Cys Peroxiredoxin, Reduced -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i81
TitleCrystal Structure of Plasmodium vivax 2-Cys Peroxiredoxin, Reduced
Components2-Cys Peroxiredoxin
KeywordsOXIDOREDUCTASE / peroxiredoxin / structural genomics consortium / SGC
Function / homology
Function and homology information


cellular response to stress / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
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 speciesPlasmodium vivax SaI-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsArtz, J.D. / Qiu, W. / Dong, A. / Lew, J. / Ren, H. / Zhao, Y. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. ...Artz, J.D. / Qiu, W. / Dong, A. / Lew, J. / Ren, H. / Zhao, Y. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal Structure of Plasmodium vivax 2-Cys Peroxiredoxin, Reduced
Authors: Artz, J.D. / Qiu, W. / Dong, A. / Lew, J. / Ren, H. / Zhao, Y. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
Remark 999 SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS UNAVAILABLE FOR THE PROTEIN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-Cys Peroxiredoxin
B: 2-Cys Peroxiredoxin
C: 2-Cys Peroxiredoxin
D: 2-Cys Peroxiredoxin
E: 2-Cys Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)118,6615
Polymers118,6615
Non-polymers00
Water1,44180
1
A: 2-Cys Peroxiredoxin
B: 2-Cys Peroxiredoxin
C: 2-Cys Peroxiredoxin
D: 2-Cys Peroxiredoxin
E: 2-Cys Peroxiredoxin

A: 2-Cys Peroxiredoxin
B: 2-Cys Peroxiredoxin
C: 2-Cys Peroxiredoxin
D: 2-Cys Peroxiredoxin
E: 2-Cys Peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)237,32110
Polymers237,32110
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Unit cell
Length a, b, c (Å)91.352, 212.575, 115.261
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
11E-202-

HOH

-
Components

#1: Protein
2-Cys Peroxiredoxin


Mass: 23732.133 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax SaI-1 (eukaryote) / Species: Plasmodium vivax / Strain: Salvador I / Plasmid: p28a-thrombin-lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-Rosetta Oxford / References: UniProt: A5K421*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 19% PEG 3350, 150 mM Li3Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 41568 / Num. obs: 41514 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 6.4 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 23.1
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.62 / Num. unique all: 2028 / Rsym value: 0.694 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H66

2h66


Resolution: 2.45→36.56 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 2107 -RANDOM
Rwork0.2173 ---
obs0.2198 39472 99.95 %-
Refinement stepCycle: LAST / Resolution: 2.45→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 0 80 7270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.025
X-RAY DIFFRACTIONr_angle_refined_deg2.231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.95
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.022
X-RAY DIFFRACTIONr_chiral_restr0.168
LS refinement shellResolution: 2.45→2.51 Å
RfactorNum. reflection% reflection
Rfree0.391 148 -
Rwork0.351 --
obs-2892 100 %

+
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