[English] 日本語
Yorodumi
- PDB-9ifh: PANDDA analysis - Crystal structure of Trypanosoma brucei trypano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ifh
TitlePANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z2856434890
ComponentsTrypanothione reductase
KeywordsOXIDOREDUCTASE / trypanothione reductase
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / kinetoplast / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / nuclear lumen / cell redox homeostasis / flavin adenine dinucleotide binding / nucleoplasm ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / kinetoplast / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / nuclear lumen / cell redox homeostasis / flavin adenine dinucleotide binding / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / 4-methyl-N-phenylpiperazine-1-carboxamide / DI(HYDROXYETHYL)ETHER / Trypanothione reductase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsExertier, C. / Antonelli, L. / Ilari, A. / Fiorillo, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery22027European Union
Citation
Journal: Front Chem Biol / Year: 2025
Title: Expanding the molecular landscape of fragments binding to trypanothione reductase, a legitimate target for drug design against human African trypanosomiasis
Authors: Exertier, C. / Antonelli, L. / Brufani, V. / Colotti, G. / Ilari, A. / Fiorillo, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trypanothione reductase
B: Trypanothione reductase
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,58629
Polymers213,9924
Non-polymers5,59425
Water16,466914
1
A: Trypanothione reductase
B: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,67614
Polymers106,9962
Non-polymers2,68012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-65 kcal/mol
Surface area37470 Å2
MethodPISA
2
C: Trypanothione reductase
D: Trypanothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,91015
Polymers106,9962
Non-polymers2,91413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-62 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.244, 63.976, 170.385
Angle α, β, γ (deg.)90.000, 97.901, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Trypanothione reductase / N(1) / N(8)-bis(glutathionyl)spermidine reductase


Mass: 53497.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The electronic density is not well enough defined to unambiguously reconstruct the N-terminal and the C-terminal extremities of the protein.
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.406.0520 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q389T8, trypanothione-disulfide reductase

-
Non-polymers , 6 types, 939 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NZD / 4-methyl-N-phenylpiperazine-1-carboxamide


Mass: 219.283 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H17N3O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 914 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12-14% PEG3350, 22-24% MPD, 40 mM imidazole pH 8.0, 50 mM NaBr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.921237 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921237 Å / Relative weight: 1
ReflectionResolution: 1.73→92.77 Å / Num. obs: 227892 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 29.38 Å2 / CC1/2: 1 / Net I/σ(I): 9.6
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 11087 / CC1/2: 0.35 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.21.2refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→82.01 Å / SU ML: 0.2593 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 11347 5 %
Rwork0.1908 215647 -
obs0.1925 226994 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.4 Å2
Refinement stepCycle: LAST / Resolution: 1.73→82.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14825 0 358 915 16098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006615795
X-RAY DIFFRACTIONf_angle_d0.83321468
X-RAY DIFFRACTIONf_chiral_restr0.05632395
X-RAY DIFFRACTIONf_plane_restr0.00662784
X-RAY DIFFRACTIONf_dihedral_angle_d15.41945947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.38683280.36956509X-RAY DIFFRACTION91.1
1.75-1.770.36253700.34327031X-RAY DIFFRACTION97.59
1.77-1.790.34853930.32627074X-RAY DIFFRACTION98.81
1.79-1.810.34143690.31327106X-RAY DIFFRACTION99.39
1.81-1.840.34163790.30337169X-RAY DIFFRACTION99.5
1.84-1.860.33083900.29117176X-RAY DIFFRACTION99.68
1.86-1.890.31363650.2837171X-RAY DIFFRACTION99.91
1.89-1.920.30073800.26867146X-RAY DIFFRACTION99.96
1.92-1.950.30233740.26557237X-RAY DIFFRACTION99.97
1.95-1.980.28663930.25247162X-RAY DIFFRACTION99.99
1.98-2.010.2633690.22977197X-RAY DIFFRACTION99.99
2.01-2.050.2613870.21827192X-RAY DIFFRACTION99.96
2.05-2.090.2853830.2177172X-RAY DIFFRACTION99.97
2.09-2.130.25583800.21087242X-RAY DIFFRACTION99.99
2.13-2.180.24443920.2067131X-RAY DIFFRACTION100
2.18-2.230.26783930.20277186X-RAY DIFFRACTION100
2.23-2.290.23783580.19997267X-RAY DIFFRACTION100
2.29-2.350.25463830.19877143X-RAY DIFFRACTION99.99
2.35-2.420.2483860.20667224X-RAY DIFFRACTION100
2.42-2.490.26093850.2037211X-RAY DIFFRACTION100
2.49-2.580.25293590.20477246X-RAY DIFFRACTION100
2.58-2.690.23963750.1987265X-RAY DIFFRACTION99.99
2.69-2.810.25013970.19917197X-RAY DIFFRACTION100
2.81-2.960.24293900.20447202X-RAY DIFFRACTION100
2.96-3.140.24953880.19627251X-RAY DIFFRACTION100
3.14-3.380.20923770.18837281X-RAY DIFFRACTION100
3.38-3.730.19393640.17247299X-RAY DIFFRACTION100
3.73-4.260.17233960.14867313X-RAY DIFFRACTION100
4.26-5.370.15183810.13357332X-RAY DIFFRACTION99.99
5.37-82.010.16613630.15457515X-RAY DIFFRACTION99.61

+
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