[English] 日本語
Yorodumi
- PDB-8d1r: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d1r
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with inhibitor SGT520
ComponentsN-acetyltransferase Eis
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / resistance / aminoglycoside / enzyme / inhibitor / acetyl transfer / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated suppression of host programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / N-acetyltransferase activity ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated suppression of host programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / bacterial extracellular vesicle / symbiont-mediated perturbation of host programmed cell death / N-acetyltransferase activity / biological process involved in interaction with host / host cell cytoplasmic vesicle / protein-lysine-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / host extracellular space / response to antibiotic / identical protein binding / cytosol
Similarity search - Function
N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
1-{3-[(4-chlorophenyl)methoxy]phenyl}methanamine / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPang, A.H. / Punetha, A. / Garneau-Tsodikova, S. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090048 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Discovery of substituted benzyloxy-benzylamine inhibitors of acetyltransferase Eis and their anti-mycobacterial activity.
Authors: Pang, A.H. / Green, K.D. / Chandrika, N.T. / Garzan, A. / Punetha, A. / Holbrook, S.Y.L. / Willby, M.J. / Posey, J.E. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3393
Polymers45,9991
Non-polymers3402
Water2,792155
1
A: N-acetyltransferase Eis
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)278,03418
Polymers275,9956
Non-polymers2,03912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area23020 Å2
ΔGint-54 kcal/mol
Surface area89670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.102, 175.102, 124.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein N-acetyltransferase Eis / Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N- ...Aminoglycoside N-acetyltransferase / Enhanced intracellular survival protein / Protein-lysine N-acetyltransferase


Mass: 45999.113 Da / Num. of mol.: 1 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PVF / 1-{3-[(4-chlorophenyl)methoxy]phenyl}methanamine


Mass: 247.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClNO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 8.5, 9.5-10% w/v PEG 8000, and 500 mM (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 37172 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.8
Reflection shellResolution: 2.19→2.24 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 1835 / CC1/2: 0.952 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.19→43.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 1893 5.1 %RANDOM
Rwork0.1732 ---
obs0.1748 35276 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.33 Å2 / Biso mean: 36.864 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.56 Å2-0 Å2
2---1.13 Å2-0 Å2
3---3.66 Å2
Refinement stepCycle: final / Resolution: 2.19→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 23 155 3225
Biso mean--61.65 37.42 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133150
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172979
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.6454281
X-RAY DIFFRACTIONr_angle_other_deg2.351.5766807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.38218.743183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1091541
X-RAY DIFFRACTIONr_chiral_restr0.0810.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023588
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02779
LS refinement shellResolution: 2.195→2.252 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 122 -
Rwork0.246 2527 -
all-2649 -
obs--96.96 %

+
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