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- PDB-6ct5: PptT PAP(CoA) 8918 complex -

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Basic information

Entry
Database: PDB / ID: 6ct5
TitlePptT PAP(CoA) 8918 complex
Components4'-phosphopantetheinyl transferase
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


enterobactin synthetase complex / enterobactin biosynthetic process / holo-[acyl-carrier-protein] synthase activity / magnesium ion binding
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
COENZYME A / Chem-FD7 / Phosphopantetheinyl transferase PptT (CoA:apo-[ACP]pantetheinephosphotransferase) (CoA:apo-[acyl-carrier protein]pantetheinephosphotransferase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75934602056 Å
AuthorsMosior, J. / Sacchettini, J. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Science / Year: 2019
Title: Opposing reactions in coenzyme A metabolism sensitizeMycobacterium tuberculosisto enzyme inhibition.
Authors: Ballinger, E. / Mosior, J. / Hartman, T. / Burns-Huang, K. / Gold, B. / Morris, R. / Goullieux, L. / Blanc, I. / Vaubourgeix, J. / Lagrange, S. / Fraisse, L. / Sans, S. / Couturier, C. / ...Authors: Ballinger, E. / Mosior, J. / Hartman, T. / Burns-Huang, K. / Gold, B. / Morris, R. / Goullieux, L. / Blanc, I. / Vaubourgeix, J. / Lagrange, S. / Fraisse, L. / Sans, S. / Couturier, C. / Bacque, E. / Rhee, K. / Scarry, S.M. / Aube, J. / Yang, G. / Ouerfelli, O. / Schnappinger, D. / Ioerger, T.R. / Engelhart, C.A. / McConnell, J.A. / McAulay, K. / Fay, A. / Roubert, C. / Sacchettini, J. / Nathan, C.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,97726
Polymers53,4092
Non-polymers3,56724
Water7,764431
1
A: 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58013
Polymers26,7051
Non-polymers1,87612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4'-phosphopantetheinyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,39613
Polymers26,7051
Non-polymers1,69212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.863, 63.408, 79.267
Angle α, β, γ (deg.)90.000, 123.149, 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
11A-616-

HOH

21A-617-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN 'A' AND (RESID 5 THROUGH 48 OR RESID 50...
211(CHAIN 'B' AND (RESID 5 THROUGH 12 OR (RESID 17...

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4'-phosphopantetheinyl transferase / Phosphopantetheinyl transferase PptT (CoA:apo-[ACP]pantetheinephosphotransferase) (CoA:apo-[acyl- ...Phosphopantetheinyl transferase PptT (CoA:apo-[ACP]pantetheinephosphotransferase) (CoA:apo-[acyl-carrier protein]pantetheinephosphotransferase)


Mass: 26704.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: CRX58_05810, ERS124361_01504 / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0T9N0I0

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Non-polymers , 6 types, 455 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-FD7 / N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea


Mass: 262.351 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H22N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: Bis-Tris Propane pH 6.7, Magnesium Sulfate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.759→39.6 Å / Num. obs: 55209 / % possible obs: 99.12 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.009804707 Å2 / CC1/2: 0.912 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.06 / Rrim(I) all: 0.126 / Net I/σ(I): 16.6
Reflection shellResolution: 1.759→1.822 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 5471 / CC1/2: 0.737 / Rpim(I) all: 0.309 / Rrim(I) all: 0.655 / % possible all: 98.54

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QJK, 4QVH

4qjk

4qvh


Resolution: 1.75934602056→39.5861996104 Å / SU ML: 0.171855888582 / Cross valid method: FREE R-VALUE / σ(F): 1.34489013578 / Phase error: 19.5464406261
RfactorNum. reflection% reflection
Rfree0.19806084936 2006 3.63346555815 %
Rwork0.160322487377 --
obs0.161648321635 55209 99.1362901778 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.3268235505 Å2
Refinement stepCycle: LAST / Resolution: 1.75934602056→39.5861996104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 181 431 3940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01230938166483714
X-RAY DIFFRACTIONf_angle_d1.311319706335084
X-RAY DIFFRACTIONf_chiral_restr0.079094324088563
X-RAY DIFFRACTIONf_plane_restr0.00756890714516640
X-RAY DIFFRACTIONf_dihedral_angle_d13.55471320442138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80330.2782957782321433725X-RAY DIFFRACTION98.0978950038
1.8033-1.85210.2683879686931343808X-RAY DIFFRACTION99.6209249431
1.8521-1.90660.225467826851483781X-RAY DIFFRACTION99.3426042984
1.9066-1.96810.2110027520281550.1671788363663775X-RAY DIFFRACTION99.4684889901
1.9681-2.03850.2172147629661380.1595638277033774X-RAY DIFFRACTION98.7380111055
2.0385-2.12010.1959999351451410.1541879663273789X-RAY DIFFRACTION99.569293134
2.1201-2.21660.205121949041480.1537023817953790X-RAY DIFFRACTION99.3440968718
2.2166-2.33340.1883854984311380.1580484481633832X-RAY DIFFRACTION99.5236901479
2.3334-2.47960.2152916064981490.1622128265553768X-RAY DIFFRACTION98.864209995
2.4796-2.6710.1991169808371430.1633734422163829X-RAY DIFFRACTION99.6737766625
2.671-2.93970.1859533532091390.1691650167943806X-RAY DIFFRACTION99.4454247542
2.9397-3.36490.1999237557131420.1629479943253810X-RAY DIFFRACTION98.6274020464
3.3649-4.23870.1964484435671410.1452656183343821X-RAY DIFFRACTION99.0747686922
4.2387-39.5860.1740469611661470.1564133883423895X-RAY DIFFRACTION98.681640625

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