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- PDB-7b4r: Structure of the 4'-phosphopantetheinyl transferase PptAb from My... -

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Basic information

Entry
Database: PDB / ID: 7b4r
TitleStructure of the 4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus in complex with Coenzyme A and N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea
ComponentsPossible 4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE / mycobacterium abscessus 4'-phosphopantetheinyl transferase complex / inhibition / amidino-urea
Function / homology
Function and homology information


enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding
Similarity search - Function
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily
Similarity search - Domain/homology
COENZYME A / Chem-FD7 / : / Possible 4'-phosphopantetheinyl transferase
Similarity search - Component
Biological speciesMycobacteroides abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsMaveyraud, L. / Carivenc, C. / Blanger, C. / Mourey, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR 16 CE18 0011 01 France
CitationJournal: Sci Rep / Year: 2021
Title: Phosphopantetheinyl transferase binding and inhibition by amidino-urea and hydroxypyrimidinethione compounds.
Authors: Carivenc, C. / Maveyraud, L. / Blanger, C. / Ballereau, S. / Roy-Camille, C. / Nguyen, M.C. / Genisson, Y. / Guilhot, C. / Chalut, C. / Pedelacq, J.D. / Mourey, L.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Possible 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5725
Polymers25,4321
Non-polymers1,1404
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-15 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.962, 83.049, 56.023
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Possible 4'-phosphopantetheinyl transferase


Mass: 25432.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus ATCC 19977 (bacteria)
Gene: MAB_3117c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1MD73
#2: Chemical ChemComp-FD7 / N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea


Mass: 262.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M LiSO4 0.1 M MES pH 6.5 20% (w/v) PEG 8K soaking 20h in 5 mM ligand 1% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→46.44 Å / Num. obs: 57619 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.82 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.049 / Rsym value: 0.045 / Net I/σ(I): 15.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 9112 / CC1/2: 0.835 / Rrim(I) all: 1.18 / Rsym value: 1.087 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.18.2_3874refinement
XSCALEdata reduction
XSCALEdata scaling
XDSdata processing
Coot0.9.2model building
DIMPLEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QYG

6qyg


Resolution: 1.4→46.44 Å / SU ML: 0.1733 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1943 2908 5.06 %
Rwork0.1618 54606 -
obs0.1634 57514 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.19 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 48 266 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01351871
X-RAY DIFFRACTIONf_angle_d1.3842578
X-RAY DIFFRACTIONf_chiral_restr0.108288
X-RAY DIFFRACTIONf_plane_restr0.0095349
X-RAY DIFFRACTIONf_dihedral_angle_d12.3198702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.44241450.4072556X-RAY DIFFRACTION98.29
1.42-1.450.41581150.32842554X-RAY DIFFRACTION97.48
1.45-1.470.34861390.29872558X-RAY DIFFRACTION97.79
1.47-1.50.33751550.27732547X-RAY DIFFRACTION97.86
1.5-1.530.26651080.24982592X-RAY DIFFRACTION98.07
1.53-1.570.25071600.22572549X-RAY DIFFRACTION97.94
1.57-1.60.22851560.18882551X-RAY DIFFRACTION98.19
1.6-1.640.22461410.16752567X-RAY DIFFRACTION98.47
1.64-1.690.21631490.15222545X-RAY DIFFRACTION98.07
1.69-1.740.18391260.13862623X-RAY DIFFRACTION98.57
1.74-1.790.1651120.12932598X-RAY DIFFRACTION97.76
1.79-1.860.17091390.13222545X-RAY DIFFRACTION97.46
1.86-1.930.17291430.14362608X-RAY DIFFRACTION98.74
1.93-2.020.16641490.13982579X-RAY DIFFRACTION98.52
2.02-2.130.16221500.13742591X-RAY DIFFRACTION98.63
2.13-2.260.17141450.14332622X-RAY DIFFRACTION98.43
2.26-2.430.17361370.14822617X-RAY DIFFRACTION98.15
2.43-2.680.20721220.15152671X-RAY DIFFRACTION99.32
2.68-3.070.18761490.16222642X-RAY DIFFRACTION98.76
3.07-3.860.20631250.16582666X-RAY DIFFRACTION97.25
3.86-46.440.18421430.1612825X-RAY DIFFRACTION98.67

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