[English] 日本語
Yorodumi
- PDB-3uy5: crystal structure of Eis from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uy5
Titlecrystal structure of Eis from Mycobacterium tuberculosis
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE / GNAT fold / acetyl transferase
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 / 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 ...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 / 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
N-acetyltransferase Eis / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, K.H. / Suh, S.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mycobacterium tuberculosis Eis protein initiates suppression of host immune responses by acetylation of DUSP16/MKP-7
Authors: Kim, K.H. / An, D.R. / Song, J. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. / Kim, K.H. / Lee, H.M. / Kim, H.J. / Jo, E.K. / Lee, J.Y. / Suh, S.W.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enhanced intracellular survival protein


Theoretical massNumber of molelcules
Total (without water)46,6451
Polymers46,6451
Non-polymers00
Water2,432135
1
A: Enhanced intracellular survival protein
x 6


Theoretical massNumber of molelcules
Total (without water)279,8696
Polymers279,8696
Non-polymers00
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_554y,x,-z-11
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area21400 Å2
ΔGint-47 kcal/mol
Surface area90330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.574, 174.574, 122.827
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

-
Components

#1: Protein Enhanced intracellular survival protein


Mass: 46644.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: eis, MT2489, MTCY253.04, Rv2416c / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS(DE3) / References: UniProt: P71727, UniProt: P9WFK7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.86 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 300mM ammonium citrate, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→20 Å / Num. obs: 26334

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.841 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1215 5.06 %
Rwork0.1828 --
obs0.1845 24011 96.53 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 110.82 Å2 / Biso mean: 32.7382 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--6.2439 Å2-0 Å20 Å2
2---6.2439 Å2-0 Å2
3---12.4877 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 135 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083122
X-RAY DIFFRACTIONf_angle_d1.1144247
X-RAY DIFFRACTIONf_dihedral_angle_d13.9571133
X-RAY DIFFRACTIONf_chiral_restr0.073476
X-RAY DIFFRACTIONf_plane_restr0.004557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.59990.27661230.2162233390
2.5999-2.7180.22991260.193240892
2.718-2.86090.23411220.1981246895
2.8609-3.03950.22931320.1836250096
3.0395-3.27330.23311530.1885252598
3.2733-3.60090.1881320.1703260799
3.6009-4.11790.20541570.1656259999
4.1179-5.17290.17731290.15862655100
5.1729-19.84190.24521410.21312701100

+
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