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- PDB-6qmh: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 6qmh
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 3-(1H-indol-3-yl)propanoic acid at 1.6A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / PPAT / Complex
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EP8 / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å
AuthorsBlaszczyk, M. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Fragment linking applied to the discovery of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase inhibitors
Authors: Blaszczyk, M. / El Bakali, J. / Boland, J.A. / Spry, C. / Dias, M. / Blundell, T.L. / Abel, C.
History
DepositionFeb 7, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 26, 2020ID: 6G7T
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1542
Polymers17,7921
Non-polymers3611
Water1,74797
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,92312
Polymers106,7546
Non-polymers2,1686
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area13820 Å2
ΔGint-99 kcal/mol
Surface area34130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.964, 98.964, 115.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-358-

HOH

31A-389-

HOH

41A-393-

HOH

51A-397-

HOH

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 17792.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: coaD, kdtB, MT3043 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPA4, 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.: 1 / Source method: obtained synthetically / Formula: C21H19N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.79 % / Description: cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MPD, CoHexamine Chloride, Cacodylate/Tris / PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.837→49.482 Å / Num. all: 19171 / Num. obs: 19171 / % possible obs: 100 % / Redundancy: 13.4 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Rsym value: 0.099 / Net I/av σ(I): 5.4 / Net I/σ(I): 17.9 / Num. measured all: 256705
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.84-1.9412.30.9640.827460.2981.0520.964100
1.94-2.0514.10.5941.326500.170.640.594100
2.05-2.2140.3492.124630.10.3740.349100
2.2-2.3713.90.2083.522980.060.2230.208100
2.37-2.613.30.1584.621270.0460.170.158100
2.6-2.9112.60.1056.719230.0310.1130.105100
2.91-3.3514.10.0758.817000.0210.0810.075100
3.35-4.1113.60.05910.514640.0170.0640.059100
4.11-5.8112.20.05310.711370.0160.0580.053100
5.81-49.48213.40.0539.66630.0160.0580.05399.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFU

1tfu


Resolution: 1.837→49.482 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.87
RfactorNum. reflection% reflection
Rfree0.2207 987 5.15 %
Rwork0.2033 --
obs0.2043 19171 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 29.93 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 1.837→49.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 44 97 1299
Biso mean--28.46 37.72 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081214
X-RAY DIFFRACTIONf_angle_d1.0341644
X-RAY DIFFRACTIONf_chiral_restr0.069187
X-RAY DIFFRACTIONf_plane_restr0.005214
X-RAY DIFFRACTIONf_dihedral_angle_d14.399441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8374-1.93430.30361340.280925702704
1.9343-2.05550.25821480.247725692717
2.0555-2.21420.26351400.218525562696
2.2142-2.4370.23181500.204425722722
2.437-2.78960.20981180.207726182736
2.7896-3.51450.22491560.198725922748
3.5145-49.49990.1921410.184327072848

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