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- PDB-8q6u: Crystal structure of a double mutant acetyltransferase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 8q6u
TitleCrystal structure of a double mutant acetyltransferase from Bacillus cereus species.
ComponentsAminoglycoside N6'-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homologyaminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminoglycoside N6'-acetyltransferase
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.516 Å
AuthorsSilvestre, H.L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PRX17/00085 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Functional and structural characterisation of RimL from Bacillus cereus, a new N alpha-acetyltransferase of ribosomal proteins that was wrongly assigned as an aminoglycosyltransferase.
Authors: Leonardo Silvestre, H. / Asensio, J.L. / Blundell, T.L. / Bastida, A. / Bolanos-Garcia, V.M.
History
DepositionAug 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside N6'-acetyltransferase
B: Aminoglycoside N6'-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,83810
Polymers39,3352
Non-polymers5038
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.573, 83.154, 53.194
Angle α, β, γ (deg.)90, 100.39, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminoglycoside N6'-acetyltransferase


Mass: 19667.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_2494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81D84
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 2mM zinc chloride, 100 mM Tris pH 8.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2010
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.516→52.321 Å / Num. obs: 31633 / % possible obs: 74.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 10.6
Reflection shellResolution: 1.516→1.636 Å / Num. unique obs: 1583 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.516→19.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1547 -RANDOM
Rwork0.1874 ---
obs0.1888 31604 57.4 %-
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.9018 Å20 Å2-0.7916 Å2
2---0.854 Å20 Å2
3----1.0478 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.516→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 26 290 3011
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012849HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043848HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1030SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it2837HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion362SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2638SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion15.95
LS refinement shellResolution: 1.52→1.59 Å
RfactorNum. reflection% reflection
Rfree0.2852 31 -
Rwork0.2343 --
obs--45.1 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6647-0.27420.68260.9858-0.21370.70420.00010.05280.06330.05280.0187-0.0390.0633-0.039-0.01880.0121-0.01560.0127-0.02480.003-0.03926.03512.2105-0.0968
20.3590.31240.44060.2842-0.10251.6453-0.0484-0.0341-0.0834-0.0341-0.01370.0061-0.08340.00610.06220.00320.0099-0.0079-0.03150.0072-0.0153-3.625616.4709-24.958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 170
2X-RAY DIFFRACTION1{ A|* }A260 - 262
3X-RAY DIFFRACTION2{ B|* }B1 - 170
4X-RAY DIFFRACTION2{ B|* }B260 - 262

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