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- PDB-5o0d: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o0d
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Phenoxymandelic acid (Fragment 4)
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
Chem-9F5 / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.539 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)52,9195
Polymers52,4313
Non-polymers4882
Water6,323351
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)105,83810
Polymers104,8616
Non-polymers9774
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14280 Å2
ΔGint-109 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.913, 125.192, 119.144
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-282-

HOH

21C-301-

HOH

31C-344-

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-9F5 / (2~{S})-2-oxidanyl-2-(3-phenoxyphenyl)ethanoic acid / 3-Phenoxymandelic acid


Mass: 244.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium Bromide 20-25% PEG 3350 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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.539→119.14 Å / Num. obs: 84215 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.056 / Rrim(I) all: 0.156 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.54-1.627.71.2690.6060.4831.359100
4.87-119.147.20.1310.9840.0510.14199.9

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.539→62.596 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2272 4391 5.22 %
Rwork0.1997 --
obs0.2012 84163 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.05 Å2 / Biso mean: 28.5212 Å2 / Biso min: 13.67 Å2
Refinement stepCycle: final / Resolution: 1.539→62.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 36 351 3908
Biso mean--40.81 36.78 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073753
X-RAY DIFFRACTIONf_angle_d1.0565125
X-RAY DIFFRACTIONf_chiral_restr0.042606
X-RAY DIFFRACTIONf_plane_restr0.005672
X-RAY DIFFRACTIONf_dihedral_angle_d12.6691388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5385-1.5560.34671490.313526512800
1.556-1.57430.33581380.298426222760
1.5743-1.59350.32521480.285126262774
1.5935-1.61370.2711290.274426312760
1.6137-1.63490.31351550.274126312786
1.6349-1.65730.29971530.261326122765
1.6573-1.6810.3051360.252226702806
1.681-1.70610.27051410.246426302771
1.7061-1.73270.22371540.230626352789
1.7327-1.76110.26881440.231926342778
1.7611-1.79150.27541250.238526622787
1.7915-1.82410.28451330.231326352768
1.8241-1.85920.27571460.223726732819
1.8592-1.89710.23381350.216126432778
1.8971-1.93840.24391560.213226432799
1.9384-1.98350.23771230.213126632786
1.9835-2.03310.23981660.212226272793
2.0331-2.08810.23151460.204926652811
2.0881-2.14950.21941450.200826512796
2.1495-2.21890.21091800.19526062786
2.2189-2.29820.2351380.187426682806
2.2982-2.39020.21061600.194526272787
2.3902-2.4990.19921540.19926752829
2.499-2.63070.24061500.204326652815
2.6307-2.79560.25631400.20326802820
2.7956-3.01140.24651510.202426702821
3.0114-3.31450.22371460.194627022848
3.3145-3.7940.18921480.183527022850
3.794-4.77980.18351310.156727522883
4.7798-62.64780.22211710.192828212992

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