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- PDB-4qb9: Crystal structure of Mycobacterium smegmatis Eis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4qb9
TitleCrystal structure of Mycobacterium smegmatis Eis in complex with paromomycin
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE / GNAT fold / SCP fold / acetyltransferase
Function / homology
Function and homology information


host cell cytoplasmic vesicle / N-acetyltransferase activity
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 / Gcn5-related N-acetyltransferase (GNAT) ...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
PAROMOMYCIN / Enhanced intracellular survival protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.293 Å
AuthorsKim, K.H. / Ahn, D.R. / Yoon, H.J. / Yang, J.K. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of Mycobacterium smegmatis Eis in complex with paromomycin.
Authors: Kim, K.H. / An, D.R. / Yoon, H.J. / Yang, J.K. / Suh, S.W.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Structure summary
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,07218
Polymers276,8026
Non-polymers4,27012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27770 Å2
ΔGint-233 kcal/mol
Surface area89400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.269, 126.536, 236.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Enhanced intracellular survival protein / Enhanced intracellular survival protein Eis


Mass: 46133.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: eis, MSMEG_3513, MSMEI_3433 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QY29
#2: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4

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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: 2.9 Å3/Da / Density % sol: 57.6 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.293→30 Å / Num. obs: 49506 / Biso Wilson estimate: 58.15 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.293→14.989 Å / FOM work R set: 0.8347 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2381 5.07 %RANDOM
Rwork0.1513 ---
obs0.1556 46928 95.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.24 Å2 / Biso mean: 48.97 Å2 / Biso min: 16.84 Å2
Refinement stepCycle: LAST / Resolution: 3.293→14.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18600 0 282 0 18882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01419362
X-RAY DIFFRACTIONf_angle_d1.69426420
X-RAY DIFFRACTIONf_chiral_restr0.0662956
X-RAY DIFFRACTIONf_plane_restr0.0083488
X-RAY DIFFRACTIONf_dihedral_angle_d16.0686910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.293-3.35950.30671370.19652400253789
3.3595-3.43170.27681450.20082495264093
3.4317-3.51050.3241390.18822518265793
3.5105-3.59710.3221350.19412512264793
3.5971-3.69290.26951270.17432523265093
3.6929-3.79990.25741380.16872523266194
3.7999-3.92040.23151180.16342540265893
3.9204-4.05790.25891270.15652569269694
4.0579-4.21690.22861540.14842586274096
4.2169-4.40420.20151410.13922623276496
4.4042-4.62990.22631260.13292660278697
4.6299-4.91030.18561520.12412699285199
4.9103-5.27410.21841660.13842686285299
5.2741-5.77710.26511290.153727562885100
5.7771-6.55120.2311430.154827752918100
6.5512-8.03630.20291500.150128022952100
8.0363-14.98940.17541540.11428803034100

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