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- PDB-6cck: Crystal structure of E.coli Phosphopantetheine Adenylyltransferas... -

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Basic information

Entry
Database: PDB / ID: 6cck
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-3-(3-chlorophenyl)-3-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)propanenitrile
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE/antibiotic / PPAT CoaD FBDD phosphopantetheine adenylyltransferase Gram-negative antibacterial antibiotic / TRANSFERASE / TRANSFERASE-antibiotic complex
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein 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
ADENOSINE-5'-TRIPHOSPHATE / Chem-EXJ / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.61 Å
AuthorsMamo, M. / Appleton, B.A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase from Gram-Negative Bacteria.
Authors: Moreau, R.J. / Skepper, C.K. / Appleton, B.A. / Blechschmidt, A. / Balibar, C.J. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Li, C. / Lindvall, M.K. / Lingel, A. / Lu, Y. / Mamo, ...Authors: Moreau, R.J. / Skepper, C.K. / Appleton, B.A. / Blechschmidt, A. / Balibar, C.J. / Benton, B.M. / Drumm, J.E. / Feng, B.Y. / Geng, M. / Li, C. / Lindvall, M.K. / Lingel, A. / Lu, Y. / Mamo, M. / Mergo, W. / Polyakov, V. / Smith, T.M. / Takeoka, K. / Uehara, K. / Wang, L. / Wei, J.R. / Weiss, A.H. / Xie, L. / Xu, W. / Zhang, Q. / de Vicente, J.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,06010
Polymers36,1482
Non-polymers1,9138
Water4,486249
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,18130
Polymers108,4436
Non-polymers5,73824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area22980 Å2
ΔGint-300 kcal/mol
Surface area33230 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)456,724120
Polymers433,77224
Non-polymers22,95196
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_454x-1/2,y+1/2,z-1/21
crystal symmetry operation14_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation15_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation16_445x-1/2,-y-1/2,-z+1/21
crystal symmetry operation17_445z-1/2,x-1/2,y+1/21
crystal symmetry operation18_454z-1/2,-x+1/2,-y-1/21
crystal symmetry operation19_555-z+1/2,-x+1/2,y+1/21
crystal symmetry operation20_544-z+1/2,x-1/2,-y-1/21
crystal symmetry operation21_544y+1/2,z-1/2,x-1/21
crystal symmetry operation22_445-y-1/2,z-1/2,-x+1/21
crystal symmetry operation23_555y+1/2,-z+1/2,-x+1/21
crystal symmetry operation24_454-y-1/2,-z+1/2,x-1/21
Buried area81670 Å2
ΔGint-785 kcal/mol
Surface area143190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.050, 135.050, 135.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 18073.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase

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Non-polymers , 5 types, 257 molecules

#2: Chemical ChemComp-EXJ / (3R)-3-(3-chlorophenyl)-3-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]propanenitrile


Mass: 328.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H13ClN6O
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.3 M ammonium sulfate, 0.2 M potassium thiocyanate, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→42.71 Å / Num. obs: 53106 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 25.47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.021 / Rrim(I) all: 0.065 / Net I/σ(I): 17.4 / Num. measured all: 505615
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.61-1.699.80.7277360.890.2420.76100
5.08-42.719.40.025176210.0080.02699.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.61→42.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2587 4.89 %RANDOM
Rwork0.176 ---
obs0.177 52895 100 %-
Displacement parametersBiso max: 99.46 Å2 / Biso mean: 27.04 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.61→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 120 249 2861
Biso mean--26.21 39.76 -
Num. residues----319
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d988SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it2840HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies19HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3639SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2840HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3899HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion14.94
LS refinement shellResolution: 1.61→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1944 190 4.87 %
Rwork0.19 3715 -
all0.1902 3905 -
obs--100 %
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)
10.6940.3007-0.2170.7065-0.56020.28950.0073-0.05940.00950.12080.02160.0622-0.0427-0.09-0.0289-0.0115-0.0023-0.0084-0.0194-0.0040.01421.3262-12.830246.7594
20.9946-0.97621.41161.6410.1161.3204-0.02790.0512-0.0597-0.0770.10190.06160.00020.0251-0.074-0.015-0.0582-0.0859-0.00240.05340.077813.9331-11.550228.6514
31.73370.2922-0.36831.8357-0.67551.340.0436-0.05580.18680.07260.09070.3495-0.0762-0.0974-0.1343-0.04980.01590.0067-0.0737-0.01450.057614.4404-7.509342.6273
42.00571.40080.23094.415-1.4662.21530.0172-0.04660.09570.0296-0.0466-0.094-0.1674-0.07010.0294-0.0203-0.00390.0023-0.0528-0.0070.009528.2944-8.143941.5578
52.64270.8435-0.06042.95090.7542.75790.02680.1978-0.3508-0.009-0.03170.0607-0.0351-0.03310.005-0.04230.0074-0.00550.0024-0.00870.030533.9771-17.05435.1217
61.08950.6589-0.40870.6521-0.07140.15860.02010.0624-0.11650.0418-0.019-0.01320.00640.01-0.0011-0.0274-0.0071-0.0281-0.02630.02430.008625.5348-21.280943.8669
71.3794-0.3578-0.23561.52841.16130.0034-0.00350.01320.0083-0.133-0.0440.0024-0.17030.13060.04760.0176-0.0243-0.01390.0040.01430.02089.5031-24.5930.8631
83.1880.20970.03471.10540.44721.05630.00070.0310.28270.0214-0.04690.18180.0882-0.18260.0462-0.0535-0.0126-0.0001-0.00360.00330.05313.3977-21.169138.1121
91.04050.6563-0.31260-0.38990.96730.0184-0.0595-0.01540.0445-0.0628-0.0448-0.08360.05450.0443-0.02330.00910.00610.0010.0037-0.0441.5618-22.8356.0703
101.7401-0.7202-0.57410.8924-0.17731.44880.0094-0.119-0.03190.0254-0.03940.0382-0.04470.24850.03-0.0347-0.004-0.00230.02450.0026-0.03447.0462-23.052155.5069
110.4124-0.60460.28691.3877-0.60551.80480.0149-0.1192-0.05880.182-0.0159-0.1522-0.0802-0.0830.0009-0.00150.00110.00370.0575-0.0132-0.028740.2832-24.862162.052
122.0539-0.3105-0.60491.33610.66610.40330.02530.1594-0.058-0.01180.0534-0.00180.0471-0.0268-0.0787-0.02930.0047-0.0129-0.02180.0207-0.040232.8502-28.439550.5784
132.20120.7892-1.89640.4701-0.60961.61350.03880.1187-0.0493-0.0198-0.0053-0.00760.0066-0.0205-0.0335-0.02580.0104-0.00650.0060.0168-0.014738.1757-22.118845.965
141.15340.7727-1.0840-0.37490.78710.0023-0.0574-0.03070.13370.00910.10010.0391-0.011-0.01130.00740.01650.01590.02290.01450.021254.761-33.201343.3854
151.6127-0.3456-0.029700.28390.65770.0149-0.2684-0.0232-0.04780.0225-0.12550.02370.1289-0.0374-0.05420.0080.01020.0430.0013-0.016460.8306-26.376946.5255
160.26070.03820.07990.0661-0.64140.2617-0.0022-0.0106-0.0007-0.0126-0.00190.01720.03250.0270.0041-0.01220.01770.0078-0.0324-0.01360.045525.8448-9.212431.8951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|37 }A1 - 37
2X-RAY DIFFRACTION2{ A|38 - A|47 }A38 - 47
3X-RAY DIFFRACTION3{ A|48 - A|73 }A48 - 73
4X-RAY DIFFRACTION4{ A|74 - A|92 }A74 - 92
5X-RAY DIFFRACTION5{ A|93 - A|109 }A93 - 109
6X-RAY DIFFRACTION6{ A|110 - A|128 }A110 - 128
7X-RAY DIFFRACTION7{ A|129 - A|138 }A129 - 138
8X-RAY DIFFRACTION8{ A|139 - A|159 }A139 - 159
9X-RAY DIFFRACTION9{ B|1 - B|15 }B1 - 15
10X-RAY DIFFRACTION10{ B|16 - B|59 }B16 - 59
11X-RAY DIFFRACTION11{ B|60 - B|80 }B60 - 80
12X-RAY DIFFRACTION12{ B|81 - B|109 }B81 - 109
13X-RAY DIFFRACTION13{ B|110 - B|128 }B110 - 128
14X-RAY DIFFRACTION14{ B|129 - B|137 }B129 - 137
15X-RAY DIFFRACTION15{ B|138 - B|159 }B138 - 159
16X-RAY DIFFRACTION16{ A|201 }A201

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