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

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Basic information

Entry
Database: PDB / ID: 6ccm
TitleCrystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with 2-((3-bromobenzyl)amino)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one
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
Chem-EXP / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 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)36,9628
Polymers36,1482
Non-polymers8146
Water5,152286
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)110,88724
Polymers108,4436
Non-polymers2,44318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation9_564y,z+1,x-11
Buried area19530 Å2
ΔGint-381 kcal/mol
Surface area35180 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
hetero molecules
x 12
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)443,54696
Polymers433,77224
Non-polymers9,77472
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_674-z+1,-x+2,y-11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_766-y+2,z+1,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_764-y+2,-z+1,x-11
crystal symmetry operation13_444x-1/2,y-1/2,z-1/21
crystal symmetry operation14_774-x+5/2,-y+5/2,z-1/21
crystal symmetry operation15_745-x+5/2,y-1/2,-z+1/21
crystal symmetry operation16_475x-1/2,-y+5/2,-z+1/21
crystal symmetry operation17_543z+1/2,x-1/2,y-3/21
crystal symmetry operation18_576z+1/2,-x+5/2,-y+3/21
crystal symmetry operation19_673-z+3/2,-x+5/2,y-3/21
crystal symmetry operation20_646-z+3/2,x-1/2,-y+3/21
crystal symmetry operation21_453y-1/2,z+1/2,x-3/21
crystal symmetry operation22_756-y+5/2,z+1/2,-x+3/21
crystal symmetry operation23_466y-1/2,-z+3/2,-x+3/21
crystal symmetry operation24_763-y+5/2,-z+3/2,x-3/21
Buried area68060 Å2
ΔGint-1113 kcal/mol
Surface area150750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.533, 135.533, 135.533
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-EXP / 2-{[(3-bromophenyl)methyl]amino}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7(6H)-one


Mass: 334.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12BrN5O
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.89 Å3/Da / Density % sol: 57.41 %
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: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.79→36.22 Å / Num. obs: 38908 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 29.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.069 / Net I/σ(I): 16.3 / Num. measured all: 237032
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.896.20.68356480.820.2990.747100
5.66-36.225.90.025130310.0110.02899.2

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.79→36.22 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1887 4.86 %RANDOM
Rwork0.169 ---
obs0.171 38822 99.5 %-
Displacement parametersBiso max: 117.55 Å2 / Biso mean: 32.22 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.79→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 45 286 2826
Biso mean--46.54 42.07 -
Num. residues----318
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d935SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes400HARMONIC5
X-RAY DIFFRACTIONt_it2697HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion352SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3473SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2697HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3677HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion15.93
LS refinement shellResolution: 1.79→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.252 138 4.59 %
Rwork0.213 2866 -
all0.215 3004 -
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)
10.6782-0.5160.96221.0625-0.15151.4292-0.0857-0.01550.04690.1056-0.0347-0.02-0.225-0.04780.1204-0.0205-0.00240.0089-0.0673-0.0025-0.0545155.708177.68454.7971
21.01960.1278-0.675800.41010.6431-0.01920.0569-0.0428-0.0496-0.0309-0.1156-0.03120.15950.05020.1721-0.1057-0.152-0.01330.0790.0128172.538186.90955.9216
32.4999-0.56081.85243.9921-1.27153.823-0.0646-0.0464-0.04160.5302-0.0742-0.0326-0.5442-0.06230.13880.14640.0079-0.0036-0.0932-0.0201-0.1129159.411183.94260.4847
42.66020.53071.11681.82060.24365.12520.0428-0.02820.12490.18610.03090.02430.25760.0044-0.07370.00670.02760.0013-0.0636-0.0037-0.0128161.43170.75257.493
53.221.4044-1.79883.5127-2.483.848-0.02330.22590.1388-0.24150.1083-0.0860.03240.0921-0.085-0.03240.0188-0.0229-0.0117-0.0551-0.0104167.829166.53148.3159
61.3324-2.1991.68254.2067-2.91042.55340.00730.06710.0427-0.10990.0188-0.1041-0.06810.0796-0.02610.0156-0.0094-0.0066-0.0044-0.0102-0.0305157.8173.90246.1798
70.8861-2.85262.91042.0838-1.9951.1181-0.0146-0.2998-0.02280.01210.0512-0.12110.0340.0544-0.03650.0163-0.0205-0.01190.03-0.02130.0752169.46191.47143.1281
80.00140.5864-0.20184.57-0.40110.6909-0.05910.0741-0.03230.54420.0031-0.2472-0.25330.0240.0560.0447-0.0164-0.029-0.08630.0041-0.0436161.837196.7947.4171
92.5105-1.4836-0.23911.4124-0.72810.00130.1145-0.0413-0.260.083-0.02710.17020.0785-0.0444-0.0875-0.07190.0145-0.0049-0.05-0.0407-0.0091147.348156.42442.7163
103.2602-1.6104-0.33972.17190.81941.35740.17260.1711-0.4738-0.0123-0.19050.23930.0223-0.12340.0179-0.06450.0027-0.0014-0.0701-0.02630.0421147.692152.06141.8566
111.7301-0.73261.54381.4983-1.29011.4972-0.00990.0256-0.24090.0470.02980.17080.081-0.1617-0.0199-0.03930.00490.01730.01920.01590.0744140.68157.95842.2266
121.1096-0.8159-0.70543.98-1.03272.0013-0.15950.11240.1727-0.43260.0741-0.37280.0999-0.09660.0854-0.004-0.02990.0171-0.0047-0.0307-0.0249151.503167.22838.1298
130.8655-0.70650.27640.6238-0.77350.3805-0.04440.07630.05540.01370.0323-0.0961-0.0295-0.02380.0121-0.02870.0001-0.0252-0.0155-0.03050.0172156.618161.31444.0174
141.8188-1.060.18731.4164-0.38741.15030.01870.04580.0176-0.0293-0.06380.0531-0.0847-0.07740.045-0.00550.0303-0.02370.0249-0.02260.0382159.983145.99231.3268
151.7771-1.1252-0.65274.6087-0.00950.6666-0.02730.0613-0.35420.0219-0.06630.53630.27370.16190.0936-0.05490.0128-0.0008-0.0917-0.02290.0802157.103139.29537.6473
160.10890.42030.11820.3432-0.02710.2110.00170.00370.02730.00320.0120.0357-0.0204-0.0151-0.0137-0.01970.07150.1431-0.04130.01480.0624170.6173.82956.1966
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|160 }A139 - 160
9X-RAY DIFFRACTION9{ B|2 - B|15 }B2 - 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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