[English] 日本語
Yorodumi
- PDB-8rx5: Mycothione reductase from M. tuberculosis with FAD and NADPH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rx5
TitleMycothione reductase from M. tuberculosis with FAD and NADPH
ComponentsMycothione reductase
KeywordsOXIDOREDUCTASE / Oxidoreductase NADPH dependent Flavoprotein
Function / homology
Function and homology information


Mycothiol metabolism / mycothione reductase / mycothione reductase [NAD(P)H] activity / mycothiol metabolic process / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / pyruvate metabolic process / NADPH binding / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Mycothione 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
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Mycothione reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsOorts, L. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
Funding support Belgium, European Union, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)I007220N Belgium
Research Foundation - Flanders (FWO)G066619N Belgium
European Union (EU)853903European Union
CitationJournal: To Be Published
Title: Structure of mycothione reductase
Authors: Oorts, L. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
History
DepositionFeb 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mycothione reductase
B: Mycothione reductase
C: Mycothione reductase
D: Mycothione reductase
E: Mycothione reductase
F: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,69616
Polymers300,0096
Non-polymers7,68710
Water543
1
A: Mycothione reductase
B: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0616
Polymers100,0032
Non-polymers3,0584
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-55 kcal/mol
Surface area34030 Å2
MethodPISA
2
C: Mycothione reductase
D: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3185
Polymers100,0032
Non-polymers2,3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-52 kcal/mol
Surface area34610 Å2
MethodPISA
3
E: Mycothione reductase
F: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3185
Polymers100,0032
Non-polymers2,3153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-54 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.171, 174.171, 260.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein
Mycothione reductase / Mycothiol-disulfide reductase / NADPH-dependent mycothione reductase


Mass: 50001.574 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mtr, gorA, Rv2855 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WHH3, mycothione reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG8000, Sodium chloride, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 3.25→77.89 Å / Num. obs: 63666 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.114 / Rrim(I) all: 0.288 / Χ2: 0.95 / Net I/σ(I): 5.7 / Num. measured all: 397206
Reflection shellResolution: 3.25→3.42 Å / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.904 / Num. measured all: 43600 / Num. unique obs: 9170 / CC1/2: 0.655 / Rpim(I) all: 0.449 / Rrim(I) all: 1.017 / Χ2: 0.88 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→77.89 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 3218 5.07 %
Rwork0.2111 --
obs0.213 63420 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→77.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21066 0 510 3 21579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222000
X-RAY DIFFRACTIONf_angle_d0.48229996
X-RAY DIFFRACTIONf_dihedral_angle_d9.1713234
X-RAY DIFFRACTIONf_chiral_restr0.0443436
X-RAY DIFFRACTIONf_plane_restr0.0053840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.30.38391490.32892543X-RAY DIFFRACTION98
3.3-3.350.34391450.30162551X-RAY DIFFRACTION99
3.35-3.40.38341430.29262552X-RAY DIFFRACTION99
3.4-3.460.30071350.28052584X-RAY DIFFRACTION100
3.46-3.520.30361500.26142576X-RAY DIFFRACTION100
3.52-3.590.3161170.26082597X-RAY DIFFRACTION100
3.59-3.670.26211470.25922586X-RAY DIFFRACTION100
3.67-3.750.26551380.24062582X-RAY DIFFRACTION100
3.75-3.830.28631580.23332565X-RAY DIFFRACTION100
3.83-3.930.30111170.23482630X-RAY DIFFRACTION100
3.93-4.030.25011380.22412609X-RAY DIFFRACTION100
4.03-4.150.21891210.19692610X-RAY DIFFRACTION100
4.15-4.290.22111510.19462600X-RAY DIFFRACTION100
4.29-4.440.22861150.19212623X-RAY DIFFRACTION100
4.44-4.620.21711310.18062634X-RAY DIFFRACTION100
4.62-4.830.20781610.1772634X-RAY DIFFRACTION100
4.83-5.080.23471120.18142622X-RAY DIFFRACTION100
5.08-5.40.22511620.20282628X-RAY DIFFRACTION100
5.4-5.820.25741430.2122642X-RAY DIFFRACTION100
5.82-6.40.22331410.21192660X-RAY DIFFRACTION99
6.4-7.330.24931570.20732652X-RAY DIFFRACTION99
7.33-9.230.19381480.15712697X-RAY DIFFRACTION99
9.23-77.890.1781390.15842825X-RAY DIFFRACTION98

+
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