[English] 日本語
Yorodumi
- PDB-6b3t: Crystal structure of acetyltransferase Eis from Mycobacterium tub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b3t
TitleCrystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with a 1,2,4-triazino[5,6b]indole-3-thioether inhibitor analogue 39b
ComponentsN-acetyltransferase Eis
Keywordstransferase/transferase inhibitor / TRANSFERASE / tuberculosis / aminoglycoside / resistance / 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 / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily ...N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / : / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Acetyltransferase (GNAT) domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CJ7 / COENZYME A / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGajadeera, C.S. / Hou, C. / Garneau-Tsodikova, S. / Ngo, H.X. / 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: ACS Infect Dis / Year: 2018
Title: Potent 1,2,4-Triazino[5,6 b]indole-3-thioether Inhibitors of the Kanamycin Resistance Enzyme Eis from Mycobacterium tuberculosis.
Authors: Ngo, H.X. / Green, K.D. / Gajadeera, C.S. / Willby, M.J. / Holbrook, S.Y.L. / Hou, C. / Garzan, A. / Mayhoub, A.S. / Posey, J.E. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionSep 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetyltransferase Eis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2315
Polymers45,9991
Non-polymers1,2324
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.547, 175.547, 120.722
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 1 types, 1 molecules A

#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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eis, Rv2416c, MTCY253.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WFK7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CJ7 / 8-fluoro-5-methyl-3-{[2-(piperidin-1-yl)ethyl]sulfanyl}-5H-[1,2,4]triazino[5,6-b]indole


Mass: 345.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20FN5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Reservoir: Tris-HCl pH 8.5 adjusted at room temperature (100 mM), PEG 8,000 (10-15% w/v), and (NH4)2SO4 (0.4 M)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27954 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 29

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1K

3r1k


Resolution: 2.4→34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.712 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23125 1414 5.1 %RANDOM
Rwork0.21645 ---
obs0.21723 26517 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.389 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 69 139 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193185
X-RAY DIFFRACTIONr_bond_other_d0.0060.023013
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9854338
X-RAY DIFFRACTIONr_angle_other_deg0.89636886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4135394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84321.348141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46415481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0351540
X-RAY DIFFRACTIONr_chiral_restr0.1670.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213579
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9024.1961583
X-RAY DIFFRACTIONr_mcbond_other0.9024.1961581
X-RAY DIFFRACTIONr_mcangle_it1.6986.2871974
X-RAY DIFFRACTIONr_mcangle_other1.6976.2871975
X-RAY DIFFRACTIONr_scbond_it0.6254.3741602
X-RAY DIFFRACTIONr_scbond_other0.6264.3771599
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1996.5282359
X-RAY DIFFRACTIONr_long_range_B_refined4.25933.2253414
X-RAY DIFFRACTIONr_long_range_B_other4.21333.1333389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 109 -
Rwork0.297 1919 -
obs--100 %

+
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