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- PDB-8qj8: Structure of Mycobacterium abscessus Phosphopantetheine adenylylt... -

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Basic information

Entry
Database: PDB / ID: 8qj8
TitleStructure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with inhibitor
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / PPAT / nucleotidyltransferase
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 Å
AuthorsThomas, S.E. / McCarthy, W.J. / Coyne, A.G. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: A Fragment-Based Competitive 19 F LB-NMR Platform For Hotspot-Directed Ligand Profiling.
Authors: McCarthy, W.J. / Thomas, S.E. / Olaleye, T. / Boland, J.A. / Floto, R.A. / Williams, G. / Blundell, T.L. / Coyne, A.G. / Abell, C.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 11, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3476
Polymers52,4313
Non-polymers9163
Water4,882271
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,69312
Polymers104,8616
Non-polymers1,8326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14230 Å2
ΔGint-107 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.723, 125.993, 118.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

21A-412-

HOH

31C-328-

HOH

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 17476.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-VIW / 3-[3-(3-azanyl-2-cyano-phenyl)indol-1-yl]propanoic acid


Mass: 305.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium bromide, PEG3350, 0.1M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.538→65.53 Å / Num. obs: 85408 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Net I/σ(I): 17.9
Reflection shellResolution: 1.54→1.62 Å / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.888 / Num. measured all: 94451 / Num. unique obs: 12304 / CC1/2: 0.836 / Rpim(I) all: 0.344 / Rrim(I) all: 0.954 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.538→43.984 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 4324 5.07 %
Rwork0.2101 --
obs0.2109 85346 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.538→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 69 271 3838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063630
X-RAY DIFFRACTIONf_angle_d1.0014924
X-RAY DIFFRACTIONf_dihedral_angle_d12.8331269
X-RAY DIFFRACTIONf_chiral_restr0.04570
X-RAY DIFFRACTIONf_plane_restr0.005639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.538-1.5550.38551590.36472603X-RAY DIFFRACTION100
1.555-1.57330.37331170.33882731X-RAY DIFFRACTION100
1.5733-1.59250.32731310.30242671X-RAY DIFFRACTION100
1.5925-1.61260.3091630.27412642X-RAY DIFFRACTION100
1.6126-1.63380.28941530.27212687X-RAY DIFFRACTION100
1.6338-1.65620.29111410.24562663X-RAY DIFFRACTION100
1.6562-1.67990.261310.25192715X-RAY DIFFRACTION100
1.6799-1.7050.32591350.24392697X-RAY DIFFRACTION100
1.705-1.73160.27591390.23752644X-RAY DIFFRACTION100
1.7316-1.760.27111220.22832707X-RAY DIFFRACTION100
1.76-1.79030.26871300.23642712X-RAY DIFFRACTION100
1.7903-1.82290.28631250.23412704X-RAY DIFFRACTION100
1.8229-1.8580.24271500.23212678X-RAY DIFFRACTION100
1.858-1.89590.22631370.22472682X-RAY DIFFRACTION100
1.8959-1.93710.26751250.22392717X-RAY DIFFRACTION100
1.9371-1.98220.21621370.22492670X-RAY DIFFRACTION100
1.9822-2.03170.22731660.22832671X-RAY DIFFRACTION100
2.0317-2.08670.26061710.22592676X-RAY DIFFRACTION100
2.0867-2.14810.21191640.21792673X-RAY DIFFRACTION100
2.1481-2.21740.23591500.212694X-RAY DIFFRACTION100
2.2174-2.29660.25751390.21562709X-RAY DIFFRACTION100
2.2966-2.38860.22961670.2212678X-RAY DIFFRACTION100
2.3886-2.49730.24351640.22132672X-RAY DIFFRACTION100
2.4973-2.62890.24741500.22532742X-RAY DIFFRACTION100
2.6289-2.79360.2231090.22312741X-RAY DIFFRACTION100
2.7936-3.00930.21941420.21642717X-RAY DIFFRACTION100
3.0093-3.3120.19511560.21752730X-RAY DIFFRACTION100
3.312-3.79110.22341530.19972739X-RAY DIFFRACTION100
3.7911-4.77540.1821390.16432782X-RAY DIFFRACTION100
4.7754-43.9840.19711590.1892875X-RAY DIFFRACTION100

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