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

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Basic information

Entry
Database: PDB / ID: 6ccs
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 2-(trifluoromethyl)-1H-benzo[d]imidazol-4-ol
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
2-(trifluoromethyl)-1H-benzimidazol-7-ol / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.06 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

Downloads & links

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0329
Polymers36,1482
Non-polymers8857
Water3,387188
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)111,09727
Polymers108,4436
Non-polymers2,65421
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area20020 Å2
ΔGint-391 kcal/mol
Surface area34210 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)444,387108
Polymers433,77224
Non-polymers10,61584
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 area69330 Å2
ΔGint-1148 kcal/mol
Surface area147570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.993, 134.993, 134.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#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
#2: Chemical ChemComp-EXD / 2-(trifluoromethyl)-1H-benzimidazol-7-ol


Mass: 202.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5F3N2O
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→42.69 Å / Num. obs: 24425 / % possible obs: 96.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.045 / Rrim(I) all: 0.099 / Net I/σ(I): 10.7 / Num. measured all: 114745
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.06-2.174.70.6541745236830.7970.3360.7372.1100
6.52-42.694.50.04437638400.9970.0230.0530.398.3

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.06→42.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1255 5.14 %RANDOM
Rwork0.191 ---
obs0.192 24395 95.9 %-
Displacement parametersBiso max: 113.75 Å2 / Biso mean: 38.23 Å2 / Biso min: 20.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 2.06→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 53 188 2732
Biso mean--44.58 43.5 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d916SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it2671HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion347SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3395SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2671HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3640HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion16.38
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.213 148 4.96 %
Rwork0.198 2836 -
all0.198 2984 -
obs--96.39 %
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)
12.41790.820.13830.8421-0.49380.92230.0304-0.20780.11420.1636-0.04420.1341-0.072-0.02040.0138-0.0309-0.0119-0.0161-0.0409-0.0142-0.005620.7608-13.149446.0608
20.2672-0.4872.1861.409-0.0230.7421-0.03760.14210.0001-0.23880.06980.1611-0.0478-0.0405-0.03220.0747-0.0607-0.1066-0.04710.0350.032914.6222-11.611728.2806
32.90010.5796-1.00254.4139-0.01861.9231-0.0505-0.01350.20780.27730.10380.5194-0.0167-0.1732-0.0533-0.07490.0373-0.0099-0.1072-0.01750.066614.5464-7.510742.2008
40-1.3263-0.47474.855-2.8861.23090.0493-0.00360.0442-0.0817-0.1425-0.0495-0.1926-0.07310.09320.0239-0.02140.0033-0.0265-0.0050.033328.1747-9.075841.6229
51.9588-0.9447-1.76972.7815-1.9085.40030.01310.1633-0.2359-0.020.01680.0746-0.3105-0.2578-0.0299-0.05280.0580.00680.0317-0.01830.002933.8568-17.238134.8611
60.40731.136-0.59272.49860.07680.00230.03880.0101-0.1743-0.0626-0.0524-0.2482-0.0420.05410.01360.00760.0064-0.0336-0.02940.0269-0.024825.6912-20.658143.7049
71.09230.30362.0361.47061.09170-0.03280.0473-0.0060.0468-0.0155-0.1297-0.0224-0.02610.0483-0.0315-0.02490.0245-0.0090.01020.03049.2693-24.976330.6308
82.8092.8532-1.90840.04522.50753.3257-0.0463-0.07030.40070.034-0.15810.54420.2909-0.30060.2044-0.0943-0.0199-0.0174-0.0389-0.03660.13023.6969-20.989737.9967
92.98232.7046-1.870-0.31173.4441-0.0067-0.10250.052-0.0442-0.2315-0.12510.01160.06360.2382-0.03820.0161-0.0171-0.00320.0087-0.062940.8963-22.352856.2317
105.2405-2.1039-2.61222.26731.172.524-0.2366-0.4976-0.26590.11620.02460.07440.12770.54420.212-0.0896-0.00310.01650.02920.0322-0.079447.4275-23.419455.5763
111.751.5016-1.53790.0029-2.19353.8508-0.0139-0.20040.02440.2660.0429-0.18520.01360.1549-0.029-0.0467-0.0131-0.01230.11730.0056-0.019740.2575-25.237761.7968
122.94510.6696-0.35843.86751.49453.13690.10660.201-0.206-0.2860.2378-0.07950.2655-0.0677-0.3444-0.04110.0033-0.046-0.04760.014-0.048732.3933-28.802350.034
133.95852.2333-1.83931.69-1.54471.03710.03360.2335-0.1407-0.1567-0.0859-0.0980.04780.00850.0523-0.02750.0131-0.0207-0.00130.0057-0.039138.1812-22.334746.2101
140.85450.7723-1.90740.8471-0.91111.43930.0088-0.0149-0.09410.09960.0231-0.0386-0.0435-0.0433-0.03190.04160.011-0.020.03020.01840.050555.0686-33.279643.1907
155.2008-1.34-1.31830.28090.31560.03440.0051-0.5442-0.2385-0.1481-0.0520.06640.15620.31160.0469-0.10630.01140.01110.01620.0286-0.074260.8738-26.317346.7267
160-0.17110.25610.10910.18610.0001-0.00270.0115-0.0106-0.0094-0.00770.00360.0039-0.00610.01040.03950.05710.0405-0.0257-0.0138-0.012628.4574-8.879932.0067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|37 }A2 - 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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