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

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Basic information

Entry
Database: PDB / ID: 6qmg
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 5-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid at 1.8A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / PPAT / Complex
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / protein hexamerization / 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
INDOLYLPROPIONIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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: 6G7V
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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)17,9822
Polymers17,7921
Non-polymers1891
Water1,31573
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,89012
Polymers106,7546
Non-polymers1,1356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area15830 Å2
ΔGint-47 kcal/mol
Surface area34820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.094, 98.094, 113.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-360-

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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: coaD, kdtB, Rv2965c, MTCY349.22, u0002e / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WPA5, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-IOP / INDOLYLPROPIONIC ACID


Mass: 189.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.94 Å3/Da / Density % sol: 58.2 % / 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: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.648→67.923 Å / Num. all: 25454 / Num. obs: 25454 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 29.04 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Rsym value: 0.067 / Net I/av σ(I): 5.1 / Net I/σ(I): 26.4 / Num. measured all: 501122
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value
1.65-1.7419.71.5890.536900.3751.6721.589
1.74-1.8419.80.8240.934900.1940.8650.824
1.84-1.9720.50.4391.632620.1010.4590.439
1.97-2.1319.90.2163.230690.050.2260.216
2.13-2.3320.10.1195.928030.0280.1250.119
2.33-2.6119.90.0868.125540.020.0910.086
2.61-3.0119.50.06110.722690.0150.0650.061
3.01-3.69190.05111.519300.0130.0550.051
3.69-5.2118.50.04712.215160.0120.0510.047
5.21-67.92317.10.04810.88710.0130.0530.048

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Processing

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

1tfu


Resolution: 1.65→67.92 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.06
RfactorNum. reflection% reflection
Rfree0.227 1295 5.09 %
Rwork0.212 --
obs0.213 25454 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.5 Å2
Refinement stepCycle: LAST / Resolution: 1.65→67.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 14 73 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071199
X-RAY DIFFRACTIONf_angle_d1.031622
X-RAY DIFFRACTIONf_dihedral_angle_d14.989437
X-RAY DIFFRACTIONf_chiral_restr0.053188
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6482-1.71420.36881360.30962694X-RAY DIFFRACTION100
1.7142-1.79220.32421360.29282646X-RAY DIFFRACTION100
1.7922-1.88670.29251480.25412662X-RAY DIFFRACTION100
1.8867-2.00490.26811370.24492652X-RAY DIFFRACTION100
2.0049-2.15980.27841410.23492652X-RAY DIFFRACTION100
2.1598-2.37710.24121580.21742668X-RAY DIFFRACTION100
2.3771-2.72110.23241560.22232687X-RAY DIFFRACTION100
2.7211-3.42830.20221420.20632697X-RAY DIFFRACTION100
3.4283-67.98050.21410.19032801X-RAY DIFFRACTION100

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