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- PDB-7yy4: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -

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Basic information

Entry
Database: PDB / ID: 7yy4
TitleCrystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 8
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-fluoranylnaphthalene-2-carboxylic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.671 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)52,8115
Polymers52,4313
Non-polymers3802
Water5,116284
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)105,62210
Polymers104,8616
Non-polymers7614
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13800 Å2
ΔGint-104 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.945, 124.900, 118.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-I7W / 6-fluoranylnaphthalene-2-carboxylic acid


Mass: 190.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H7FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 54.28 %
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: 1.67→118.95 Å / Num. obs: 64560 / % possible obs: 98.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 19.65 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.13 / Rrim(I) all: 0.364 / Net I/σ(I): 4.8 / Num. measured all: 498823
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.67-1.767.81.0897403095070.6460.4191.1682.2
5.28-118.957.30.3111649222500.9260.1210.3356.8

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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: 1.671→64.891 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 3261 5.05 %
Rwork0.2208 61259 -
obs0.2224 64520 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 25.6402 Å2 / Biso min: 9.86 Å2
Refinement stepCycle: final / Resolution: 1.671→64.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 28 284 3801
Biso mean--31.96 33.4 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073668
X-RAY DIFFRACTIONf_angle_d1.0534999
X-RAY DIFFRACTIONf_chiral_restr0.043590
X-RAY DIFFRACTIONf_plane_restr0.005654
X-RAY DIFFRACTIONf_dihedral_angle_d12.6611315
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.671-1.6960.35471230.32392730100
1.696-1.72250.35181550.31272659100
1.7225-1.75070.33391100.30132687100
1.7507-1.78090.31051290.30172714100
1.7809-1.81330.31591600.29362665100
1.8133-1.84820.28721590.26292662100
1.8482-1.88590.31151570.2392685100
1.8859-1.92690.29541120.2486197374
1.9269-1.97170.30481610.23462658100
1.9717-2.0210.26981270.23552729100
2.021-2.07570.2721390.22492701100
2.0757-2.13680.26911310.22472683100
2.1368-2.20570.25511580.22492712100
2.2057-2.28460.27411590.2215226786
2.2846-2.3760.26851510.22812688100
2.376-2.48420.27451250.22362717100
2.4842-2.61520.23941600.23172725100
2.6152-2.7790.2641440.22922697100
2.779-2.99360.23941570.21212701100
2.9936-3.29480.24221400.21352751100
3.2948-3.77160.21821390.19652760100
3.7716-4.75150.18361410.17272779100
4.7515-64.8910.24311240.21472916100

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