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- PDB-6g6v: Phosphopantetheine adenylyltransferase from Mycobacterium tubercu... -

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Basic information

Entry
Database: PDB / ID: 6g6v
TitlePhosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in complex with 4-(2-carboxybenzoyl)-2-nitrobenzoic acid at 1.9A 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
4-(2-carboxyphenyl)carbonyl-2-nitro-benzoic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.942 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
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)18,1082
Polymers17,7921
Non-polymers3151
Water97354
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)108,64612
Polymers106,7546
Non-polymers1,8916
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 area14750 Å2
ΔGint-104 kcal/mol
Surface area34080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.751, 97.751, 114.711
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-317-

HOH

21A-345-

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-EO8 / 4-(2-carboxyphenyl)carbonyl-2-nitro-benzoic acid


Mass: 315.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9NO7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 58.5 % / Description: cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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
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: 1.942→48.876 Å / Num. obs: 15776 / % possible obs: 100 % / Redundancy: 19.4 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Rsym value: 0.075 / Net I/av σ(I): 6.1 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.942-2.0519.61.4870.522620.3521.5651.487100
2.05-2.17200.787121690.1840.8240.787100
2.17-2.3219.90.3991.820200.0930.4180.399100
2.32-2.5120.40.2622.719030.060.2730.262100
2.51-2.7519.80.164.517430.0370.1670.16100
2.75-3.0719.60.097.915870.0210.0950.09100
3.07-3.5519.30.06210.613950.0150.0660.062100
3.55-4.3417.90.05111.612030.0130.0550.051100
4.34-6.1417.70.043149430.0110.0460.043100
6.14-48.87616.50.04213.25510.0110.0450.04299.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TFU

1tfu


Resolution: 1.942→47.483 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.219 787 4.99 %
Rwork0.1867 --
obs0.1883 15775 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.42 Å2 / Biso mean: 41.8 Å2 / Biso min: 20.28 Å2
Refinement stepCycle: final / Resolution: 1.942→47.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 29 54 1241
Biso mean--52.84 46.69 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071201
X-RAY DIFFRACTIONf_angle_d0.991626
X-RAY DIFFRACTIONf_chiral_restr0.074186
X-RAY DIFFRACTIONf_plane_restr0.004214
X-RAY DIFFRACTIONf_dihedral_angle_d20.018450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9418-2.06350.30331400.249724582598
2.0635-2.22280.2311400.193524462586
2.2228-2.44650.23981220.187924882610
2.4465-2.80050.24291360.188524892625
2.8005-3.52810.19331230.192925042627
3.5281-47.49760.20981260.177426032729
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.63120.6472-0.51831.51360.66921.41290.00710.5658-0.6383-0.19750.03510.08990.2090.02050.02650.3683-0.0232-0.01720.3208-0.13530.38-5.610231.87664.7504
20.3310.2408-0.02720.1830.09740.22070.0373-0.83730.1752-0.3611-0.19290.60740.398-1.15470.0060.3901-0.0969-0.11740.4579-0.02760.3353-19.513836.23715.7724
30.7445-0.3274-0.12571.8829-1.07251.0534-0.2230.14770.5032-0.1833-0.0381-0.2681-0.05330.1968-0.00080.2498-0.0096-0.05750.2944-0.02020.2554-10.861446.053312.9815
4-0.0854-0.06010.03840.1009-0.12970.24750.1925-0.1004-0.11580.06040.429-0.05540.1689-0.627-0.00080.32570.0013-0.02260.32810.01840.34616.787539.140913.8755
51.62591.4721-0.61160.74130.15470.7621-0.18020.533-0.5364-0.21790.302-0.28560.11270.15760.00380.391-0.0010.08670.4383-0.15160.407111.060735.9744-0.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )A1 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 83 )A73 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 117 )A84 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 126 )A118 - 126
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 157 )A127 - 157

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