[English] 日本語
Yorodumi
- PDB-9fov: Crystal structure of Tryparedoxin from Trypanosoma cruzi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fov
TitleCrystal structure of Tryparedoxin from Trypanosoma cruzi
ComponentsTryparedoxin, putative
KeywordsOXIDOREDUCTASE / Thioredoxin superfamily Trypanothione Electron transport
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus
Similarity search - Function
TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Tryparedoxin, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSchindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Tryparedoxin from Trypanosoma cruzi
Authors: Schindelin, H.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryparedoxin, putative
B: Tryparedoxin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5673
Polymers32,4752
Non-polymers921
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-3 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.463, 30.403, 74.910
Angle α, β, γ (deg.)90.000, 106.820, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

21A-444-

HOH

31B-357-

HOH

-
Components

#1: Protein Tryparedoxin, putative


Mass: 16237.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053509997.30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D1B8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M Ammoniumcitrate Protein concentration: 6.8 mg/ml 25 mM Na-phosphate buffer, pH 7.5, 150 mM NaCl 1 microliter of protein plus 1 microliter of reservoir

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.25→40.52 Å / Num. obs: 73970 / % possible obs: 98.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4 % / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3604 / CC1/2: 0.517 / Rpim(I) all: 0.648 / Rrim(I) all: 1.405 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→35.85 Å / SU ML: 0.1757 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 1809 2.45 %
Rwork0.1675 72038 -
obs0.1682 73847 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.36 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 6 387 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382689
X-RAY DIFFRACTIONf_angle_d0.74353717
X-RAY DIFFRACTIONf_chiral_restr0.0705417
X-RAY DIFFRACTIONf_plane_restr0.0069473
X-RAY DIFFRACTIONf_dihedral_angle_d13.23641028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.35471340.31795424X-RAY DIFFRACTION96.28
1.28-1.320.34071310.27995444X-RAY DIFFRACTION97.19
1.32-1.360.30751380.25455406X-RAY DIFFRACTION96.64
1.36-1.410.26211270.22335472X-RAY DIFFRACTION97.61
1.41-1.470.26871360.2085597X-RAY DIFFRACTION99.15
1.47-1.540.23751280.18625522X-RAY DIFFRACTION98.62
1.54-1.620.21781380.15655557X-RAY DIFFRACTION98.39
1.62-1.720.19371280.155508X-RAY DIFFRACTION98.39
1.72-1.850.17841520.14715502X-RAY DIFFRACTION97.9
1.85-2.040.17831370.14735539X-RAY DIFFRACTION97.46
2.04-2.330.17981550.1445622X-RAY DIFFRACTION99.16
2.33-2.940.15571460.15325645X-RAY DIFFRACTION99.16
2.94-35.850.17021590.15295800X-RAY DIFFRACTION98.81

+
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