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- PDB-5o08: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o08
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with Dephospho-coenzyme A
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
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 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)54,74210
Polymers52,4313
Non-polymers2,3117
Water6,413356
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)109,48320
Polymers104,8616
Non-polymers4,62214
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area25330 Å2
ΔGint-169 kcal/mol
Surface area32780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.046, 124.828, 116.189
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-352-

HOH

21A-418-

HOH

31C-343-

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-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H35N7O13P2S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM Sodium fluoride 0.1M Bis-Tris propane pH 6.5 20% PEG3350
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→64.94 Å / Num. obs: 78718 / % possible obs: 98.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 19.3 / Num. measured all: 588063 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.55-1.647.50.78786665114840.80.3020.8442.3
4.91-64.947.10.0251916126980.9990.010.02756.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O06

5o06


Resolution: 1.552→43.299 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 4035 5.13 %
Rwork0.1985 74643 -
obs0.2 78678 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.89 Å2 / Biso mean: 29.2034 Å2 / Biso min: 15.04 Å2
Refinement stepCycle: final / Resolution: 1.552→43.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 148 356 4062
Biso mean--24.21 35.81 -
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073814
X-RAY DIFFRACTIONf_angle_d1.1015193
X-RAY DIFFRACTIONf_chiral_restr0.04603
X-RAY DIFFRACTIONf_plane_restr0.005660
X-RAY DIFFRACTIONf_dihedral_angle_d12.6421355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5524-1.57070.29411290.285325412670100
1.5707-1.58980.29631210.269926232744100
1.5898-1.60990.28541580.265525452703100
1.6099-1.63110.29721370.262725852722100
1.6311-1.65350.28171470.256926162763100
1.6535-1.67710.25861440.250825222666100
1.6771-1.70210.23721370.235625882725100
1.7021-1.72870.2561450.237326112756100
1.7287-1.75710.32411580.239925652723100
1.7571-1.78740.25981330.235925912724100
1.7874-1.81990.30171410.2325922733100
1.8199-1.85490.26341260.230926142740100
1.8549-1.89270.28341170.235426022719100
1.8927-1.93390.25061590.224425652724100
1.9339-1.97890.24131340.224226202754100
1.9789-2.02840.29921490.218625802729100
2.0284-2.08320.30111040.22852048215278
2.0832-2.14450.21891450.212625932738100
2.1445-2.21370.26581450.211726122757100
2.2137-2.29280.26441310.20572190232185
2.2928-2.38460.22161490.210525892738100
2.3846-2.49320.24561220.20826482770100
2.4932-2.62460.20071400.209726312771100
2.6246-2.7890.26671320.206626172749100
2.789-3.00430.20651430.201926142757100
3.0043-3.30650.24161310.197226722803100
3.3065-3.78470.19291310.17826482779100
3.7847-4.76740.1861740.15126502824100
4.7674-43.31560.20051530.175127712924100

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