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- PDB-5o0a: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o0a
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 5-methyl-1-phenyl-pyrazole-4-carboxylic acid (Fragment 1)
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Coenzyme A Biosynthesis
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP 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
5-methyl-1-phenyl-pyrazole-4-carboxylic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsThomas, S.E. / Kim, S.Y. / Mendes, V. / Blaszczyk, M. / Blundell, T.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cystic Fibrosis Trust United Kingdom
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew.
Authors: Thomas, S.E. / Mendes, V. / Kim, S.Y. / Malhotra, S. / Ochoa-Montano, B. / Blaszczyk, M. / Blundell, T.L.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.title
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0376
Polymers52,4313
Non-polymers6073
Water5,206289
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,07512
Polymers104,8616
Non-polymers1,2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14200 Å2
ΔGint-106 kcal/mol
Surface area35150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.244, 125.247, 119.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21C-301-

HOH

31C-332-

HOH

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Components

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


Mass: 17476.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-9FH / 5-methyl-1-phenyl-pyrazole-4-carboxylic acid


Mass: 202.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H10N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium bromide 20-25% PEG3350 0.1M Bis-Tris propane
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.805→65.13 Å / Num. obs: 52663 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Net I/σ(I): 20.4
Reflection shellResolution: 1.805→2.08 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.473 / CC1/2: 0.94 / Rpim(I) all: 0.204 / Rrim(I) all: 0.528 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.1data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.805→65.126 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2295 2431 4.62 %
Rwork0.2049 --
obs0.206 52623 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.94 Å2 / Biso mean: 30.2441 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 1.805→65.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 45 289 3829
Biso mean--33.85 36.09 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083620
X-RAY DIFFRACTIONf_angle_d1.0534917
X-RAY DIFFRACTIONf_chiral_restr0.043576
X-RAY DIFFRACTIONf_plane_restr0.005642
X-RAY DIFFRACTIONf_dihedral_angle_d14.8041302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8054-1.84230.31031400.281829513091
1.8423-1.88230.2821280.262829093037
1.8823-1.92610.28511510.245929053056
1.9261-1.97430.29571500.239329063056
1.9743-2.02770.29251550.22629313086
2.0277-2.08730.26431610.22228923053
2.0873-2.15470.22031340.213129553089
2.1547-2.23170.23971320.208129113043
2.2317-2.32110.24331460.210329343080
2.3211-2.42670.27391370.214629543091
2.4267-2.55470.2171270.213429573084
2.5547-2.71470.24211170.220329963113
2.7147-2.92430.21151210.216529603081
2.9243-3.21860.22631940.212429153109
3.2186-3.68430.2481560.197929753131
3.6843-4.64170.18611390.168330033142
4.6417-65.16830.20051430.191831383281

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