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- PDB-5o0b: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o0b
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Bromo-1H-indazole-5-carboxylic acid (Fragment 2)
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
3-bromanyl-1~{H}-indazole-5-carboxylic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.735 Å
AuthorsThomas, S.E. / Kim, S.Y. / Mendes, V. / Blaszczyk, M. / Blundell, T.L.
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)53,8779
Polymers52,4313
Non-polymers1,4466
Water4,954275
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)107,75418
Polymers104,8616
Non-polymers2,89212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14120 Å2
ΔGint-109 kcal/mol
Surface area35100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.069, 125.171, 119.435
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-366-

HOH

21C-302-

HOH

31C-338-

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-9FE / 3-bromanyl-1~{H}-indazole-5-carboxylic acid


Mass: 241.041 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H5BrN2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 54.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium bromide 20-25% PEG3350 0.1MBis-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: 1.73→65.01 Å / Num. obs: 59232 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 22.15 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.083 / Rrim(I) all: 0.233 / Net I/σ(I): 7.7 / Num. measured all: 457527 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.73-1.837.71.2720.5530.4871.364100
5.49-65.017.20.170.980.0660.18399.9

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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: 1.735→59.718 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.2293 2916 4.93 %
Rwork0.1975 --
obs0.1991 59188 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.4 Å2 / Biso mean: 29.0105 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.735→59.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 78 275 3864
Biso mean--47.66 35.9 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073851
X-RAY DIFFRACTIONf_angle_d1.0285267
X-RAY DIFFRACTIONf_chiral_restr0.044610
X-RAY DIFFRACTIONf_plane_restr0.005689
X-RAY DIFFRACTIONf_dihedral_angle_d14.751419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7347-1.76320.32251330.303526092742
1.7632-1.79360.36121310.310226702801
1.7936-1.82620.34851300.292926612791
1.8262-1.86130.28221260.295826682794
1.8613-1.89930.34721340.276826592793
1.8993-1.94060.30841440.24726522796
1.9406-1.98570.28391360.21626522788
1.9857-2.03540.24521190.208626882807
2.0354-2.09040.2671370.208626652802
2.0904-2.1520.23341310.196426742805
2.152-2.22140.22091210.193926762797
2.2214-2.30080.22411460.19126552801
2.3008-2.39290.27641380.200626602798
2.3929-2.50180.21351620.197326652827
2.5018-2.63380.23951590.195526452804
2.6338-2.79880.22411530.194926722825
2.7988-3.01480.2231530.187226822835
3.0148-3.31820.22311490.182527072856
3.3182-3.79830.21481500.173626972847
3.7983-4.78520.17481500.157927382888
4.7852-59.75290.20091140.198928772991

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