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- PDB-7yy8: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -

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Basic information

Entry
Database: PDB / ID: 7yy8
TitleCrystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 12
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
3-(INDOL-3-YL) LACTATE / (2R)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.516 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)52,8415
Polymers52,4313
Non-polymers4102
Water6,089338
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)105,68210
Polymers104,8616
Non-polymers8214
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14660 Å2
ΔGint-95 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.894, 125.022, 119.163
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-283-

HOH

21C-341-

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-3IL / 3-(INDOL-3-YL) LACTATE / (2S)-2-HYDROXY-3-(1H-INDOL-3-YL)PROPANOIC ACID


Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4Z9 / (2R)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid


Mass: 205.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.516→119.16 Å / Num. obs: 87328 / % possible obs: 99.6 % / Redundancy: 7.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.039 / Rrim(I) all: 0.109 / Net I/σ(I): 11.9
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
1.52-1.67.81.09298224125360.7280.4111.1682.598.9
4.79-119.167.20.0842120929660.9920.0330.09123.999.9

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Phasing

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

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHASER2.5.7phasing
PHENIX1.9refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.516→56.979 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 4500 5.15 %
Rwork0.2078 82800 -
obs0.2092 87300 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.67 Å2 / Biso mean: 28.1458 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.516→56.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 30 338 3866
Biso mean--35.8 37.67 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073669
X-RAY DIFFRACTIONf_angle_d1.0754996
X-RAY DIFFRACTIONf_chiral_restr0.041587
X-RAY DIFFRACTIONf_plane_restr0.005654
X-RAY DIFFRACTIONf_dihedral_angle_d13.5211333
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5163-1.53350.31521170.3093274899
1.5335-1.55160.29621350.2925272799
1.5516-1.57050.31211420.2845271199
1.5705-1.59040.33351390.2784271999
1.5904-1.61130.28281330.2691273199
1.6113-1.63340.29131510.2699269399
1.6334-1.65670.31991480.2652272499
1.6567-1.68140.28851690.2575274699
1.6814-1.70770.28881510.2564273499
1.7077-1.73570.27961430.247272199
1.7357-1.76570.32591330.2537274699
1.7657-1.79780.27961750.251272199
1.7978-1.83230.27151760.245271499
1.8323-1.86970.27331430.2218273299
1.8697-1.91040.24131410.22842776100
1.9104-1.95480.25571630.2242271499
1.9548-2.00370.23981510.22442747100
2.0037-2.05790.24071500.21432768100
2.0579-2.11850.23061560.21042771100
2.1185-2.18690.25531340.20892759100
2.1869-2.2650.24721690.20342746100
2.265-2.35570.23181850.20832772100
2.3557-2.46290.22131610.21052729100
2.4629-2.59280.23461610.20592793100
2.5928-2.75520.24651750.20832747100
2.7552-2.96790.21991380.20312814100
2.9679-3.26660.19061420.20052809100
3.2666-3.73920.20471520.19272820100
3.7392-4.71060.23171070.16652910100
4.7106-56.9790.21121600.20022958100

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