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- PDB-3uy5: crystal structure of Eis from Mycobacterium tuberculosis -

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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


modulation by symbiont of host programmed cell death / effector-mediated defense to host-produced reactive oxygen species / modulation by symbiont of host inflammatory response / suppression by symbiont of host defense-related programmed cell death / modulation by symbiont of host innate immune response / aminoglycoside N-acetyltransferase activity / aminoglycoside antibiotic catabolic process / bacterial extracellular vesicle / Suppression of autophagy / host extracellular space ...modulation by symbiont of host programmed cell death / effector-mediated defense to host-produced reactive oxygen species / modulation by symbiont of host inflammatory response / suppression by symbiont of host defense-related programmed cell death / modulation by symbiont of host innate immune response / aminoglycoside N-acetyltransferase activity / aminoglycoside antibiotic catabolic process / bacterial extracellular vesicle / Suppression of autophagy / host extracellular space / biological process involved in interaction with host / host cell cytoplasmic vesicle / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / identical protein binding / cytosol
Similarity search - Function
N-acetyltransferase Eis / Acetyltransferase (GNAT) domain / Eis-like, acetyltransferase domain / Enhanced intracellular survival protein domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) ...N-acetyltransferase Eis / Acetyltransferase (GNAT) domain / Eis-like, acetyltransferase domain / Enhanced intracellular survival protein domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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