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

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Basic information

Entry
Database: PDB / ID: 8qix
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: 1.579 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)53,3005
Polymers52,4313
Non-polymers8692
Water5,513306
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)106,59910
Polymers104,8616
Non-polymers1,7384
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13140 Å2
ΔGint-102 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.443, 124.053, 118.267
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-280-

HOH

21C-340-

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-VJ7 / 3-(3-methylindol-1-yl)-~{N}-(4-phenoxyphenyl)sulfonyl-propanamide


Mass: 434.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 24% PEG3350, 0.1 M Bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9121 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9121 Å / Relative weight: 1
ReflectionResolution: 1.579→64.46 Å / Num. obs: 76170 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Χ2: 0.94 / Net I/σ(I): 14.7
Reflection shellResolution: 1.58→1.66 Å / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 3.286 / Num. measured all: 115533 / Num. unique obs: 10995 / CC1/2: 0.372 / Rpim(I) all: 1.059 / Rrim(I) all: 3.454 / Χ2: 0.84 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.579→64.459 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 3730 4.92 %
Rwork0.2113 --
obs0.2122 75883 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.579→64.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 62 306 3887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073676
X-RAY DIFFRACTIONf_angle_d1.0254998
X-RAY DIFFRACTIONf_dihedral_angle_d14.4951309
X-RAY DIFFRACTIONf_chiral_restr0.038580
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5794-1.59940.38981380.35582566X-RAY DIFFRACTION97
1.5994-1.62040.37341210.33382593X-RAY DIFFRACTION97
1.6204-1.64260.34311300.33322639X-RAY DIFFRACTION99
1.6426-1.66610.37341420.3262629X-RAY DIFFRACTION100
1.6661-1.6910.32671410.31462641X-RAY DIFFRACTION99
1.691-1.71740.32941270.30452659X-RAY DIFFRACTION100
1.7174-1.74560.31411370.29772635X-RAY DIFFRACTION100
1.7456-1.77570.31751610.29182647X-RAY DIFFRACTION100
1.7757-1.8080.32621520.27132640X-RAY DIFFRACTION100
1.808-1.84270.25951460.23962648X-RAY DIFFRACTION100
1.8427-1.88040.25921290.24612668X-RAY DIFFRACTION100
1.8804-1.92120.2231320.23632673X-RAY DIFFRACTION100
1.9212-1.96590.2321300.22812668X-RAY DIFFRACTION100
1.9659-2.01510.24021230.22592698X-RAY DIFFRACTION100
2.0151-2.06960.26871400.22262651X-RAY DIFFRACTION100
2.0696-2.13050.23761370.21112686X-RAY DIFFRACTION100
2.1305-2.19930.24011320.21272668X-RAY DIFFRACTION100
2.1993-2.27790.24981140.20472695X-RAY DIFFRACTION100
2.2779-2.36910.25761340.2142673X-RAY DIFFRACTION100
2.3691-2.47690.2431570.21852668X-RAY DIFFRACTION100
2.4769-2.60750.26331170.21892715X-RAY DIFFRACTION100
2.6075-2.77090.26031550.21972668X-RAY DIFFRACTION100
2.7709-2.98480.19271180.21122715X-RAY DIFFRACTION100
2.9848-3.28520.20541320.21552740X-RAY DIFFRACTION100
3.2852-3.76050.20561820.18452674X-RAY DIFFRACTION100
3.7605-4.73760.18391460.16262750X-RAY DIFFRACTION100
4.7376-64.4590.19921570.18782846X-RAY DIFFRACTION100

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