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- PDB-6c30: Mycobacterium smegmatis RimJ (apo form) -

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Basic information

Entry
Database: PDB / ID: 6c30
TitleMycobacterium smegmatis RimJ (apo form)
ComponentsGNAT family acetyltransferase
KeywordsTRANSFERASE / GNAT / N-acetyltransferase
Function / homologyAcetyltransferase (GNAT) domain / N-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / GNAT family acetyltransferase
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.397 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

Downloads & links

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Assembly

Deposited unit
A: GNAT family acetyltransferase
B: GNAT family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,70611
Polymers48,0472
Non-polymers6599
Water12,358686
1
A: GNAT family acetyltransferase
hetero molecules

B: GNAT family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,70611
Polymers48,0472
Non-polymers6599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area3890 Å2
ΔGint-42 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.414, 79.408, 116.156
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 GNAT family acetyltransferase


Mass: 24023.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: ydaF_1, ERS451418_05295 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6IYM9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24 % w/v polyethylene glycol 1500, 20 % v/v glycerol

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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: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.397→50 Å / Num. obs: 748457 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 25.3
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 103579 / CC1/2: 0.772 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.397→28.207 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.84
RfactorNum. reflection% reflection
Rfree0.1951 2000 1.93 %
Rwork0.1739 --
obs0.1743 103496 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.397→28.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 39 686 4010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063467
X-RAY DIFFRACTIONf_angle_d1.1294727
X-RAY DIFFRACTIONf_dihedral_angle_d11.8051243
X-RAY DIFFRACTIONf_chiral_restr0.044513
X-RAY DIFFRACTIONf_plane_restr0.006607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3974-1.43240.25721370.25076962X-RAY DIFFRACTION97
1.4324-1.47110.23961410.23537151X-RAY DIFFRACTION100
1.4711-1.51440.2631420.22127184X-RAY DIFFRACTION100
1.5144-1.56320.25161420.20237208X-RAY DIFFRACTION100
1.5632-1.61910.22021420.1917198X-RAY DIFFRACTION100
1.6191-1.68390.18141420.18487212X-RAY DIFFRACTION100
1.6839-1.76060.2511420.18317222X-RAY DIFFRACTION100
1.7606-1.85340.20951420.17637223X-RAY DIFFRACTION100
1.8534-1.96950.19861430.1747262X-RAY DIFFRACTION100
1.9695-2.12150.18531430.16587258X-RAY DIFFRACTION100
2.1215-2.33490.17031450.17077302X-RAY DIFFRACTION100
2.3349-2.67250.21391430.17977313X-RAY DIFFRACTION100
2.6725-3.36620.21031460.17457403X-RAY DIFFRACTION100
3.3662-28.21270.16071500.15367598X-RAY DIFFRACTION99

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