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- PDB-7ywm: Crystal structure of Mycobacterium abcessus Phosphopantetheine ad... -

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Basic information

Entry
Database: PDB / ID: 7ywm
TitleCrystal structure of Mycobacterium abcessus Phosphopantetheine adenylyltransferase in complex with ATP
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.624 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 14, 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)54,0259
Polymers52,4313
Non-polymers1,5946
Water6,377354
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)108,05018
Polymers104,8616
Non-polymers3,18912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area19590 Å2
ΔGint-173 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.827, 125.134, 119.083
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-367-

HOH

21A-431-

HOH

31C-345-

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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium bromide 20-25% PEG3350 0.1M 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: 1.62→119.08 Å / Num. obs: 71526 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.036 / Rrim(I) all: 0.1 / Net I/σ(I): 11.7 / Num. measured all: 503579
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
1.62-1.716.10.72863335103070.8210.3110.7942.3100
5.14-119.0870.0741716124360.9940.030.0823.899.8

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Phasing

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

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Processing

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

5o06


Resolution: 1.624→64.85 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 3656 5.12 %
Rwork0.1863 67815 -
obs0.1876 71471 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.14 Å2 / Biso mean: 30.1994 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: final / Resolution: 1.624→64.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 96 354 3986
Biso mean--28.62 39.61 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073865
X-RAY DIFFRACTIONf_angle_d1.2425304
X-RAY DIFFRACTIONf_chiral_restr0.052620
X-RAY DIFFRACTIONf_plane_restr0.006684
X-RAY DIFFRACTIONf_dihedral_angle_d16.0481427
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.624-1.64530.30021470.26942547
1.6453-1.66780.25251310.25452577
1.6678-1.69160.28161220.24472599
1.6916-1.71690.26931210.23662594
1.7169-1.74370.24381270.22542616
1.7437-1.77230.25621450.23242553
1.7723-1.80290.29141380.22672600
1.8029-1.83570.27481540.22612580
1.8357-1.8710.26991570.21762574
1.871-1.90920.24611440.20962583
1.9092-1.95070.23391260.20472592
1.9507-1.99610.22021280.19462621
1.9961-2.0460.21121420.1922583
2.046-2.10130.22481470.1972595
2.1013-2.16310.22851410.18472586
2.1631-2.2330.21451680.1822587
2.233-2.31280.22311600.18032575
2.3128-2.40540.16391210.18692622
2.4054-2.51490.23991280.18942641
2.5149-2.64740.21611150.19272630
2.6474-2.81330.23811240.19292659
2.8133-3.03050.22061400.19082629
3.0305-3.33550.18931550.1892613
3.3355-3.81810.21211670.17072626
3.8181-4.81020.16221530.15072668
4.8102-64.850.19671550.18182765

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