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- PDB-6c37: Mycobacterium smegmatis RimJ in complex with CoA-disulfide -

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Basic information

Entry
Database: PDB / ID: 6c37
TitleMycobacterium smegmatis RimJ in complex with CoA-disulfide
ComponentsAcetyltransferase, GNAT family protein
KeywordsTRANSFERASE / GNAT / N-acetyltransferase
Function / homology: / protein-N-terminal-alanine acetyltransferase activity / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / cytoplasm / Chem-5NG / Acetyltransferase, GNAT family protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.696 Å
AuthorsFavrot, L. / Hegde, S.S. / Blanchard, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI060899 United States
CitationJournal: To Be Published
Title: Structural Characterization of Mycobacterium smegmatis RimJ, an N-acetyltransferase protein
Authors: Favrot, L. / Hegde, S.S. / Blanchard, J.S.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase, GNAT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5752
Polymers23,0411
Non-polymers1,5331
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.131, 64.131, 230.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

#1: Protein Acetyltransferase, GNAT family protein


Mass: 23041.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5469 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R3G9
#2: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 mM sodium chloride, 0.1 M sodium potassium phosphate (pH 6.2) and 10 % w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.696→50 Å / Num. obs: 53962 / % possible obs: 91.6 % / Redundancy: 11.5 % / Net I/σ(I): 19.7
Reflection shellResolution: 1.696→1.8 Å / Rmerge(I) obs: 0.961 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.696→31.761 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1475 5.03 %
Rwork0.1922 --
obs0.1933 53957 91.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→31.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 74 201 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071743
X-RAY DIFFRACTIONf_angle_d1.0062385
X-RAY DIFFRACTIONf_dihedral_angle_d10.159989
X-RAY DIFFRACTIONf_chiral_restr0.062252
X-RAY DIFFRACTIONf_plane_restr0.006298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6955-1.72630.31031500.2712864X-RAY DIFFRACTION97
1.7263-1.75950.2931470.24562819X-RAY DIFFRACTION97
1.7595-1.79540.2831520.24122870X-RAY DIFFRACTION97
1.7954-1.83450.21311610.22282882X-RAY DIFFRACTION97
1.8345-1.87710.30151480.24952851X-RAY DIFFRACTION97
1.8771-1.92410.3329590.26631150X-RAY DIFFRACTION97
1.9241-1.97610.34871340.32472556X-RAY DIFFRACTION87
1.9761-2.03420.24611500.20042868X-RAY DIFFRACTION98
2.0342-2.09990.25251550.21652901X-RAY DIFFRACTION98
2.0999-2.17490.23151510.18982876X-RAY DIFFRACTION98
2.1749-2.2620.1915960.19861731X-RAY DIFFRACTION98
2.262-2.36490.24211460.20742798X-RAY DIFFRACTION96
2.3649-2.48950.25811490.19062899X-RAY DIFFRACTION99
2.4895-2.64540.25821480.20832917X-RAY DIFFRACTION99
2.6454-2.84960.21691570.20242907X-RAY DIFFRACTION99
2.8496-3.13610.23691560.18692915X-RAY DIFFRACTION99
3.1361-3.58940.22681520.1842951X-RAY DIFFRACTION99
3.5894-4.52020.13181460.15022578X-RAY DIFFRACTION88
4.5202-31.76630.15881560.1652911X-RAY DIFFRACTION99

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