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- PDB-4mfj: The crystal structure of acyltransferase -

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Basic information

Entry
Database: PDB / ID: 4mfj
TitleThe crystal structure of acyltransferase
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
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein tcp24


Theoretical massNumber of molelcules
Total (without water)39,2711
Polymers39,2711
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.5, 105.5, 133.9
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Putative uncharacterized protein tcp24 / acyltransferase


Mass: 39271.410 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 5.48 Å3/Da / Density % sol: 77.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 2.5M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97893 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 18553 / Num. obs: 17598 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.3 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.335 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22853 955 5.1 %RANDOM
Rwork0.18017 ---
obs0.18267 17598 98.75 %-
all-18553 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.699 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å21.78 Å2-0 Å2
2--3.56 Å2-0 Å2
3----5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 53 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192728
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9513715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9821.971137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59815423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5441531
X-RAY DIFFRACTIONr_chiral_restr0.1060.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212168
LS refinement shellResolution: 2.893→2.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 69 -
Rwork0.328 1258 -
obs--97.72 %

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