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- PDB-7yy2: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -

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Basic information

Entry
Database: PDB / ID: 7yy2
TitleCrystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Compound 20
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / PPAT / Nucleotidyltransferase / Coenzyme A biosynthesis
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
Chem-EP8 / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.598 Å
AuthorsThomas, S.E. / Coyne, A.G. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design.
Authors: Thomas, S.E. / McCarthy, W.J. / El Bakali, J. / Brown, K.P. / Kim, S.Y. / Blaszczyk, M. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / Blundell, T.L.
History
DepositionFeb 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: 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: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5156
Polymers52,4313
Non-polymers1,0843
Water5,765320
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)107,03012
Polymers104,8616
Non-polymers2,1686
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13680 Å2
ΔGint-103 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.285, 125.970, 119.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-374-

HOH

21A-434-

HOH

31C-329-

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-EP8 / 5-[3-(1~{H}-indol-3-yl)propoxy]-1-phenyl-pyrazole-4-carboxylic acid


Mass: 361.394 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H19N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium bromide, 20-24 % 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: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.598→119.55 Å / Num. obs: 76321 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 21.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.846.70.57177845265120.9330.2360.6183.6100
3.2-119.556.50.0266399198490.9990.0110.02864.999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASER2.5.6phasing
PHENIX1.9refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.598→55.724 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 3687 4.83 %
Rwork0.1832 72580 -
obs0.1843 76267 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.68 Å2 / Biso mean: 30.9337 Å2 / Biso min: 10.34 Å2
Refinement stepCycle: final / Resolution: 1.598→55.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 81 320 3897
Biso mean--22.65 39.46 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073700
X-RAY DIFFRACTIONf_angle_d1.0385038
X-RAY DIFFRACTIONf_chiral_restr0.044586
X-RAY DIFFRACTIONf_plane_restr0.005654
X-RAY DIFFRACTIONf_dihedral_angle_d14.5131347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.598-1.61870.27291470.2632743100
1.6187-1.64090.29311420.25892763100
1.6409-1.66440.30421430.25612765100
1.6644-1.68920.29051450.25272755100
1.6892-1.71560.29471740.24812732100
1.7156-1.74370.26091470.23342763100
1.7437-1.77380.2651470.21752774100
1.7738-1.80610.23141310.21122784100
1.8061-1.84080.23351440.20532775100
1.8408-1.87840.22221410.18852727100
1.8784-1.91920.22951420.18942783100
1.9192-1.96390.22251550.1892760100
1.9639-2.0130.21761360.19342777100
2.013-2.06740.22831450.18822797100
2.0674-2.12820.21071130.18742811100
2.1282-2.19690.20531290.17032772100
2.1969-2.27550.20981350.16652800100
2.2755-2.36660.19121590.17872778100
2.3666-2.47430.19961690.17812761100
2.4743-2.60470.24751330.18352816100
2.6047-2.76790.22951470.18812787100
2.7679-2.98160.20641290.18482829100
2.9816-3.28160.20831340.18572828100
3.2816-3.75640.17921240.1782842100
3.7564-4.73230.16181230.15312902100
4.7323-55.7240.17651530.1779295699
Refinement TLS params.Method: refined / Origin x: -12.264 Å / Origin y: -21.754 Å / Origin z: -25.8785 Å
111213212223313233
T0.0959 Å20.0266 Å20.0043 Å2-0.135 Å2-0.0165 Å2--0.1315 Å2
L0.1311 °20.0567 °2-0.1613 °2-0.2363 °2-0.1286 °2--0.6092 °2
S-0.0006 Å °-0.0146 Å °-0.0079 Å °0.0392 Å °-0.0154 Å °0.0666 Å °-0.0417 Å °-0.1917 Å °0.0026 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 157
2X-RAY DIFFRACTION1allB1 - 157
3X-RAY DIFFRACTION1allC1 - 158
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allW1 - 320

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