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

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Basic information

Entry
Database: PDB / ID: 8qiy
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: 1.5149 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

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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)52,9735
Polymers52,4313
Non-polymers5422
Water5,495305
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)105,94610
Polymers104,8616
Non-polymers1,0854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14180 Å2
ΔGint-107 kcal/mol
Surface area35340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.307, 125.586, 119.243
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-341-

HOH

21C-229-

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-VCC / 1-(2-aminophenyl)-5-(trifluoromethyl)pyrazole-4-carboxylic acid


Mass: 271.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium bromide, 24% PEG3350, 0.1 M 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→65.21 Å / Num. obs: 88990 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.025 / Rrim(I) all: 0.076 / Χ2: 0.84 / Net I/σ(I): 14.1 / Num. measured all: 811948
Reflection shellResolution: 1.51→1.6 Å / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 3.042 / Num. measured all: 119620 / Num. unique obs: 12895 / CC1/2: 0.475 / Rpim(I) all: 1.048 / Rrim(I) all: 3.22 / Χ2: 0.71 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5149→65.21 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2993 --
Rwork0.2752 --
obs-88329 99.28 %
Refinement stepCycle: LAST / Resolution: 1.5149→65.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 38 305 3851

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