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

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Basic information

Entry
Database: PDB / ID: 6qmi
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 3-(1H-indol-1-yl)propanoic acid at 1.7A 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
5-methyl-1-phenyl-pyrazole-4-carboxylic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 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: 6G7S
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)17,9952
Polymers17,7921
Non-polymers2021
Water1,40578
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)107,96812
Polymers106,7546
Non-polymers1,2136
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 area11730 Å2
ΔGint-85 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.994, 97.994, 113.956
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-332-

HOH

21A-361-

HOH

31A-370-

HOH

41A-378-

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-9FH / 5-methyl-1-phenyl-pyrazole-4-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.96 Å3/Da / Density % sol: 58.43 % / 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.781→34.032 Å / Num. obs: 20290 / % possible obs: 99.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 34.42 Å2 / Rpim(I) all: 0.012 / Rrim(I) all: 0.036 / Rsym value: 0.031 / Net I/av σ(I): 13.6 / Net I/σ(I): 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.781-1.888.40.7341.129190.290.840.734100
1.88-1.998.30.3991.927800.1570.4550.399100
1.99-2.138.30.1963.926290.0770.2240.196100
2.13-2.38.30.1047.424270.0410.1190.104100
2.3-2.528.40.06611.522570.0260.0750.066100
2.52-2.828.40.0418.320330.0160.0470.04100
2.82-3.258.30.02626.218240.010.030.02699.9
3.25-3.988.20.0229.315320.0080.0230.0299.9
3.98-5.6380.01732.211990.0070.0210.01799.5
5.63-34.0327.60.0223.66900.0090.0250.0299.2

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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: 1.781→34.032 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.34
RfactorNum. reflection% reflection
Rfree0.2824 1040 5.13 %
Rwork0.2455 --
obs0.2473 20289 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.87 Å2 / Biso mean: 41.1592 Å2 / Biso min: 20.63 Å2
Refinement stepCycle: final / Resolution: 1.781→34.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 15 78 1210
Biso mean--39.66 44.68 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081157
X-RAY DIFFRACTIONf_angle_d1.0981566
X-RAY DIFFRACTIONf_chiral_restr0.051182
X-RAY DIFFRACTIONf_plane_restr0.005204
X-RAY DIFFRACTIONf_dihedral_angle_d14.536423
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7812-1.87510.41511610.338626902851100
1.8751-1.99260.40221500.320827222872100
1.9926-2.14640.34871450.29927482893100
2.1464-2.36240.33141530.281527262879100
2.3624-2.70410.32411610.275127322893100
2.7041-3.40640.27411390.243727832922100
3.4064-34.03840.22331310.21262848297999

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