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- PDB-3ryo: Crystal Structure of Enhanced Intracellular Survival (Eis) Protei... -

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Basic information

Entry
Database: PDB / ID: 3ryo
TitleCrystal Structure of Enhanced Intracellular Survival (Eis) Protein from Mycobacterium tuberculosis with Acetyl CoA
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE / GNAT / Acetyltransferase
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / N-acetyltransferase activity / biological process involved in interaction with host / host cell cytoplasmic vesicle / peptide-lysine-N-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 / 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 / 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
ACETYL COENZYME *A / N-acetyltransferase Eis / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKim, K.H. / An, D.R. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Song, J. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. ...Kim, K.H. / An, D.R. / Yoon, J.Y. / Kim, H.S. / Yoon, H.J. / Song, J. / Im, H.N. / Kim, J. / Kim, D.J. / Lee, S.J. / Kim, H.J. / Lee, J.Y. / 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
DepositionMay 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhanced intracellular survival protein
B: Enhanced intracellular survival protein
C: Enhanced intracellular survival protein
D: Enhanced intracellular survival protein
E: Enhanced intracellular survival protein
F: Enhanced intracellular survival protein
G: Enhanced intracellular survival protein
H: Enhanced intracellular survival protein
I: Enhanced intracellular survival protein
J: Enhanced intracellular survival protein
K: Enhanced intracellular survival protein
L: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)574,51724
Polymers564,80212
Non-polymers9,71512
Water8,701483
1
A: Enhanced intracellular survival protein
B: Enhanced intracellular survival protein
C: Enhanced intracellular survival protein
D: Enhanced intracellular survival protein
E: Enhanced intracellular survival protein
F: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,25912
Polymers282,4016
Non-polymers4,8576
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30130 Å2
ΔGint-42 kcal/mol
Surface area88490 Å2
MethodPISA
2
G: Enhanced intracellular survival protein
H: Enhanced intracellular survival protein
I: Enhanced intracellular survival protein
J: Enhanced intracellular survival protein
K: Enhanced intracellular survival protein
L: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,25912
Polymers282,4016
Non-polymers4,8576
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30420 Å2
ΔGint-36 kcal/mol
Surface area88060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.129, 150.190, 184.383
Angle α, β, γ (deg.)90.000, 103.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enhanced intracellular survival protein


Mass: 47066.848 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: eis, Rv2416c, MT2489, MTCY253.04 / Production host: Escherichia coli (E. coli) / References: UniProt: P71727, UniProt: P9WFK7*PLUS
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.37 % / Description: THE FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12%(w/v) PEG 3350, 300mM ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 269936

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.937 Å / Occupancy max: 1 / Occupancy min: 0.62 / FOM work R set: 0.8348 / SU ML: 0.39 / σ(F): 0 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 13184 5 %Random
Rwork0.1918 ---
obs0.1946 263856 93.36 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å
Solvent model: 1. FLAT BULK SOLVENT MODEL 2. THE FILE CONTAINS FRIEDEL PAIRS
Bsol: 20.532 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 170.02 Å2 / Biso mean: 40.1862 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--7.34 Å20 Å2-4.503 Å2
2--2.0563 Å2-0 Å2
3---5.2837 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36636 0 612 483 37731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838100
X-RAY DIFFRACTIONf_angle_d1.2351912
X-RAY DIFFRACTIONf_chiral_restr0.0765772
X-RAY DIFFRACTIONf_plane_restr0.0056720
X-RAY DIFFRACTIONf_dihedral_angle_d19.7414328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7976-2.89750.32425710.2553112901186184
2.8975-3.01340.31036040.2202119231252789
3.0134-3.15040.29556270.2178120491267690
3.1504-3.31630.27096290.2039124461307593
3.3163-3.52380.25516430.1882125511319494
3.5238-3.79540.25167240.1864126441336895
3.7954-4.17640.23256930.1784127291342295
4.1764-4.77870.21556620.1621129181358096
4.7787-6.01260.22587330.185132461397999
6.0126-29.93910.23287060.1999135401424699

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