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- PDB-4mfk: The crystal structure of acyltransferase in complex with decanoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 4mfk
TitleThe crystal structure of acyltransferase in complex with decanoyl-CoA
ComponentsPutative uncharacterized protein tcp24
KeywordsTRANSFERASE / GNAT / acyltransferase / acyl-CoA
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
decanoyl-CoA / Acyltransferase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Huang, C.J. / Li, T.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Multiple complexes of long aliphatic N-acyltransferases lead to synthesis of 2,6-diacylated/2-acyl-substituted glycopeptide antibiotics, effectively killing vancomycin-resistant enterococcus
Authors: Lyu, S.Y. / Liu, Y.C. / Chang, C.Y. / Huang, C.J. / Chiu, Y.H. / Huang, C.M. / Hsu, N.S. / Lin, K.H. / Wu, C.J. / Tsai, M.D. / Li, T.L.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: Putative uncharacterized protein tcp24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4145
Polymers39,2041
Non-polymers1,2104
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.542, 133.542, 49.401
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 Putative uncharacterized protein tcp24 / acyltransferase


Mass: 39204.344 Da / Num. of mol.: 1 / Mutation: 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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-MFK / decanoyl-CoA


Mass: 921.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H54N7O17P3S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1mM MES, 0.2M ammonium sulphate, 30%(V/V) PEG5000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 23, 2012
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 39938 / Num. obs: 37919 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFJ

4mfj


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.58 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20223 2004 5 %RANDOM
Rwork0.16417 ---
obs0.16611 37919 99.68 %-
all-39938 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.46 Å20 Å2
2---0.92 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 74 464 3140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022836
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.9783881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00121.929140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222241
LS refinement shellResolution: 1.898→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 129 -
Rwork0.206 2577 -
obs--97.2 %

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