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- PDB-6iix: The crystal structure of acyltransferase mutant, orf11*-W163A, in... -

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Basic information

Entry
Database: PDB / ID: 6iix
TitleThe crystal structure of acyltransferase mutant, orf11*-W163A, in complex with octanoyl-CoA
Componentsacyltransferase
KeywordsTRANSFERASE / antibiotics
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Aminopeptidase - #120 / N-acyltransferase, N-terminal domain / GNAT-like C-terminal domain / N-acyltransferase N-terminal domain / GNAT-like C-terminal domain / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTANOYL-COENZYME A / Acyltransferase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsLi, T.L. / Huang, C.M.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Teicoplanin Reprogrammed with the N-Acyl-Glucosamine Pharmacophore at the Penultimate Residue of Aglycone Acquires Broad-Spectrum Antimicrobial Activities Effectively Killing Gram-Positive and -Negative Pathogens.
Authors: Huang, C.M. / Lyu, S.Y. / Lin, K.H. / Chen, C.L. / Chen, M.H. / Shih, H.W. / Hsu, N.S. / Lo, I.W. / Wang, Y.L. / Li, Y.S. / Wu, C.J. / Li, T.L.
History
DepositionOct 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1754
Polymers39,0891
Non-polymers1,0863
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-20 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.536, 132.536, 48.598
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein acyltransferase


Mass: 39089.211 Da / Num. of mol.: 1 / Mutation: W163A,H196A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70AY4
#2: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.3-6.5, 0.2M Ammonium Sulfate, 35% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 51038 / % possible obs: 99.8 % / Redundancy: 5.3 % / Net I/σ(I): 27.1
Reflection shellResolution: 1.73→1.79 Å / Num. unique obs: 5049 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFL

4mfl


Resolution: 1.73→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.149 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21233 2554 5.1 %RANDOM
Rwork0.18967 ---
obs0.1908 47806 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 67 326 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192806
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9813838
X-RAY DIFFRACTIONr_angle_other_deg0.97535905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2285337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96821.942139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8781533
X-RAY DIFFRACTIONr_chiral_restr0.0870.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02632
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4212.1421310
X-RAY DIFFRACTIONr_mcbond_other1.4212.1421309
X-RAY DIFFRACTIONr_mcangle_it2.2393.2041640
X-RAY DIFFRACTIONr_mcangle_other2.2393.2041641
X-RAY DIFFRACTIONr_scbond_it1.9332.4431496
X-RAY DIFFRACTIONr_scbond_other1.9172.4051489
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1353.5152180
X-RAY DIFFRACTIONr_long_range_B_refined5.67826.6473350
X-RAY DIFFRACTIONr_long_range_B_other5.29125.8833262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.731→1.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 144 -
Rwork0.282 3023 -
obs--84.93 %

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