[English] 日本語
Yorodumi
- PDB-7ndm: Crystal structure of the heterocyclic toxin methyltransferase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ndm
TitleCrystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis with bound substrate 4-hydroxyisoquinolin-1(2H)-one
ComponentsHeterocyclic toxin methyltransferase (Rv0560c)
KeywordsTRANSFERASE / Methyltransferase / HQNO-detoxification / SAM-dependent / 1 / 4-dihydroxyisoqunioline
Function / homology
Function and homology information


2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase / response to salicylic acid / cellular response to iron ion starvation / methyltransferase activity / methylation / response to hypoxia / cytosol
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
MALONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / 4-oxidanyl-2~{H}-isoquinolin-1-one / 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDenkhaus, L. / Sartor, P. / Einsle, O. / Gerhardt, S. / Fetzner, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 383/25-1 Germany
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis.
Authors: Sartor, P. / Denkhaus, L. / Gerhardt, S. / Einsle, O. / Fetzner, S.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 6, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heterocyclic toxin methyltransferase (Rv0560c)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1377
Polymers26,4201
Non-polymers7176
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-25 kcal/mol
Surface area9760 Å2
Unit cell
Length a, b, c (Å)70.337, 70.337, 97.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Heterocyclic toxin methyltransferase (Rv0560c)


Mass: 26420.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv / Gene: Rv0560c / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysSRARE / References: UniProt: P9WKL5

-
Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-U8N / 4-oxidanyl-2~{H}-isoquinolin-1-one


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.3 M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.348→60.914 Å / Num. obs: 51446 / % possible obs: 93.3 % / Redundancy: 19.9 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.084 / Rrim(I) all: 0.273 / Net I/σ(I): 12.1
Reflection shellResolution: 1.348→1.445 Å / Num. unique obs: 2574 / CC1/2: 0.49 / % possible all: 47.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BGG

7bgg


Resolution: 1.35→19.08 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2574 5.01 %RANDOM
Rwork0.166 ---
obs0.167 51416 82.5 %-
Displacement parametersBiso mean: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.3013 Å20 Å20 Å2
2---0.3013 Å20 Å2
3---0.6026 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.35→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 48 327 2000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011765HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d602SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it1765HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.43
X-RAY DIFFRACTIONt_other_torsion13.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2430SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.4 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2525 -6.41 %
Rwork0.2123 963 -
all0.2148 1029 -
obs--14.66 %
Refinement TLS params.Method: refined / Origin x: 24.7836 Å / Origin y: -19.4341 Å / Origin z: -12.9593 Å
111213212223313233
T-0.0244 Å2-0.0008 Å20.0052 Å2--0.0229 Å20.0028 Å2---0.0174 Å2
L0.4134 °20.0903 °2-0.0212 °2-0.7699 °2-0.293 °2--0.5927 °2
S0.0088 Å °0.0246 Å °0.0111 Å °-0.0164 Å °-0.0228 Å °-0.0232 Å °0.0153 Å °-0.0106 Å °0.014 Å °
Refinement TLS groupSelection details: { A|* }

+
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