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- PDB-7yy6: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -

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Basic information

Entry
Database: PDB / ID: 7yy6
TitleCrystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 10
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
6-methylpyridine-2,3-dicarboxylic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.506 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

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)52,9746
Polymers52,4313
Non-polymers5433
Water6,269348
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)105,94812
Polymers104,8616
Non-polymers1,0876
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13310 Å2
ΔGint-100 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.095, 124.936, 118.366
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-401-

HOH

21C-325-

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-I7S / 6-methylpyridine-2,3-dicarboxylic acid


Mass: 181.145 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
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: 1.506→64.99 Å / Num. obs: 89086 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 18.2
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
1.51-1.686.30.508158868250840.920.2180.5533.2100
3.37-64.996.50.0375395182880.9980.0160.0448.699.9

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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: 1.506→64.989 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2139 4491 5.04 %
Rwork0.1945 84540 -
obs0.1955 89031 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.7 Å2 / Biso mean: 26.1102 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 1.506→64.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 39 348 3892
Biso mean--29.82 34.04 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073604
X-RAY DIFFRACTIONf_angle_d1.0214888
X-RAY DIFFRACTIONf_chiral_restr0.039572
X-RAY DIFFRACTIONf_plane_restr0.005640
X-RAY DIFFRACTIONf_dihedral_angle_d13.0861293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5064-1.52350.30111360.27472809
1.5235-1.54150.28381460.2532789
1.5415-1.56030.28161550.25482786
1.5603-1.580.25981430.23622805
1.58-1.60080.23481540.23332783
1.6008-1.62270.25851510.22462794
1.6227-1.64590.26421510.22642752
1.6459-1.67050.23981390.22192822
1.6705-1.69660.23851440.20972833
1.6966-1.72440.21761480.21092760
1.7244-1.75410.23751510.21432794
1.7541-1.7860.23461450.22062831
1.786-1.82040.24371540.20892774
1.8204-1.85760.20451580.20412795
1.8576-1.89790.24561390.20872791
1.8979-1.94210.25131550.20322804
1.9421-1.99070.22041470.2072818
1.9907-2.04450.25041360.19542843
2.0445-2.10470.21821480.19962787
2.1047-2.17260.2611850.20242784
2.1726-2.25020.23681520.18722817
2.2502-2.34030.22281260.19372823
2.3403-2.44690.21591360.19772868
2.4469-2.57590.24661690.19612792
2.5759-2.73730.20121270.19792872
2.7373-2.94860.21251660.19752819
2.9486-3.24530.20291600.19452837
3.2453-3.71490.18161630.18322860
3.7149-4.68020.15391340.15972912
4.6802-64.9890.22181730.19062986

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