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- PDB-7n8m: PptT PAP(CoA) 8978B complex -

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Basic information

Entry
Database: PDB / ID: 7n8m
TitlePptT PAP(CoA) 8978B complex
Components4'-phosphopantetheinyl transferase PptT
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Structural Genomics / PSI-Biology / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


siderophore metabolic process / enterobactin synthetase complex / holo-[acyl-carrier-protein] synthase / enterobactin biosynthetic process / siderophore biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding / plasma membrane
Similarity search - Function
Enterobactin synthetase-like, component D / 4'-phosphopantetheinyl transferase, N-terminal domain / 4'-phosphopantetheinyl transferase N-terminal domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily
Similarity search - Domain/homology
Chem-17I / COENZYME A / 4'-phosphopantetheinyl transferase PptT
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMosior, J.W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas.
Authors: Ottavi, S. / Scarry, S.M. / Mosior, J. / Ling, Y. / Roberts, J. / Singh, A. / Zhang, D. / Goullieux, L. / Roubert, C. / Bacque, E. / Lagiakos, H.R. / Vendome, J. / Moraca, F. / Li, K. / ...Authors: Ottavi, S. / Scarry, S.M. / Mosior, J. / Ling, Y. / Roberts, J. / Singh, A. / Zhang, D. / Goullieux, L. / Roubert, C. / Bacque, E. / Lagiakos, H.R. / Vendome, J. / Moraca, F. / Li, K. / Perkowski, A.J. / Ramesh, R. / Bowler, M.M. / Tracy, W. / Feher, V.A. / Sacchettini, J.C. / Gold, B.S. / Nathan, C.F. / Aube, J.
History
DepositionJun 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4'-phosphopantetheinyl transferase PptT
B: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26419
Polymers53,4092
Non-polymers2,85517
Water8,197455
1
A: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,12010
Polymers26,7051
Non-polymers1,4159
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4'-phosphopantetheinyl transferase PptT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1449
Polymers26,7051
Non-polymers1,4408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.759, 63.709, 79.669
Angle α, β, γ (deg.)90.000, 123.334, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-620-

HOH

21B-621-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPRO(chain 'A' and (resid 5 through 12 or resid 18...AA5 - 125 - 12
12ASPASPARGARG(chain 'A' and (resid 5 through 12 or resid 18...AA18 - 4818 - 48
13ASNASNARGARG(chain 'A' and (resid 5 through 12 or resid 18...AA50 - 6050 - 60
14ALAALAASPASP(chain 'A' and (resid 5 through 12 or resid 18...AA62 - 6462 - 64
15LEULEUPROPRO(chain 'A' and (resid 5 through 12 or resid 18...AA66 - 7266 - 72
16LEULEUPROPRO(chain 'A' and (resid 5 through 12 or resid 18...AA74 - 8474 - 84
17VALVALARGARG(chain 'A' and (resid 5 through 12 or resid 18...AA88 - 10588 - 105
18ALAALAPHEPHE(chain 'A' and (resid 5 through 12 or resid 18...AA107 - 153107 - 153
19LYSLYSILEILE(chain 'A' and (resid 5 through 12 or resid 18...AA156 - 178156 - 178
110PHEPHELEULEU(chain 'A' and (resid 5 through 12 or resid 18...AA180 - 207180 - 207
111THRTHRGLUGLU(chain 'A' and (resid 5 through 12 or resid 18...AA209 - 217209 - 217
112GLYGLYALAALA(chain 'A' and (resid 5 through 12 or resid 18...AA219 - 228219 - 228
213THRTHRPROPRO(chain 'B' and (resid 5 through 12 or resid 18...BB5 - 125 - 12
214ASPASPARGARG(chain 'B' and (resid 5 through 12 or resid 18...BB18 - 4818 - 48
215ASNASNARGARG(chain 'B' and (resid 5 through 12 or resid 18...BB50 - 6050 - 60
216ALAALAASPASP(chain 'B' and (resid 5 through 12 or resid 18...BB62 - 6462 - 64
217LEULEUPROPRO(chain 'B' and (resid 5 through 12 or resid 18...BB66 - 7266 - 72
218LEULEUPROPRO(chain 'B' and (resid 5 through 12 or resid 18...BB74 - 8474 - 84
219VALVALARGARG(chain 'B' and (resid 5 through 12 or resid 18...BB88 - 10588 - 105
220ALAALAPHEPHE(chain 'B' and (resid 5 through 12 or resid 18...BB107 - 153107 - 153
221LYSLYSILEILE(chain 'B' and (resid 5 through 12 or resid 18...BB156 - 178156 - 178
222PHEPHELEULEU(chain 'B' and (resid 5 through 12 or resid 18...BB180 - 207180 - 207
223THRTHRGLUGLU(chain 'B' and (resid 5 through 12 or resid 18...BB209 - 217209 - 217
224GLYGLYALAALA(chain 'B' and (resid 5 through 12 or resid 18...BB219 - 228219 - 228

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4'-phosphopantetheinyl transferase PptT / PPTase


Mass: 26704.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pptT, Rv2794c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O33336, holo-[acyl-carrier-protein] synthase

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Non-polymers , 6 types, 472 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-17I / N-(2,6-diethylphenyl)-N'-(N-methylcarbamimidoyl)urea


Mass: 248.324 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H20N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1 M Bis-Tris Propane pH 6.7, 1.8M Magnesium Sulfate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.57→39.79 Å / Num. obs: 78467 / % possible obs: 99.61 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.74 Å2 / CC1/2: 0.949 / Net I/σ(I): 27.8
Reflection shellResolution: 1.57→1.625 Å / Num. unique obs: 7824 / CC1/2: 0.779 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIXdev_3126refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CT5

6ct5


Resolution: 1.57→39.79 Å / SU ML: 0.1596 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8075 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 2855 3.64 %
Rwork0.1716 75610 -
obs0.1727 78465 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.61 Å2
Refinement stepCycle: LAST / Resolution: 1.57→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 137 455 3943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933752
X-RAY DIFFRACTIONf_angle_d0.99295148
X-RAY DIFFRACTIONf_chiral_restr0.0575566
X-RAY DIFFRACTIONf_plane_restr0.0061659
X-RAY DIFFRACTIONf_dihedral_angle_d14.45762176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.26791500.23743744X-RAY DIFFRACTION99.44
1.6-1.630.25471350.2213797X-RAY DIFFRACTION99.52
1.63-1.660.25241420.21383719X-RAY DIFFRACTION99.43
1.66-1.690.24251360.21353773X-RAY DIFFRACTION99.64
1.69-1.730.25481520.20163779X-RAY DIFFRACTION99.67
1.73-1.770.22171410.20253768X-RAY DIFFRACTION99.64
1.77-1.810.26471490.19483729X-RAY DIFFRACTION99.82
1.81-1.860.23171280.18573794X-RAY DIFFRACTION99.82
1.86-1.920.20921520.1813768X-RAY DIFFRACTION99.87
1.92-1.980.20651460.17953790X-RAY DIFFRACTION99.97
1.98-2.050.1991430.16853780X-RAY DIFFRACTION100
2.05-2.130.19811370.16863789X-RAY DIFFRACTION99.97
2.13-2.230.19781500.16883757X-RAY DIFFRACTION100
2.23-2.350.1841370.1723844X-RAY DIFFRACTION100
2.35-2.490.21511510.17453781X-RAY DIFFRACTION100
2.49-2.680.19861400.17743784X-RAY DIFFRACTION100
2.68-2.950.18191420.17723807X-RAY DIFFRACTION100
2.95-3.380.19751440.16713826X-RAY DIFFRACTION100
3.38-4.260.17321390.15363821X-RAY DIFFRACTION99.57
4.26-39.790.20861410.16073760X-RAY DIFFRACTION96.15

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