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- PDB-5o0c: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o0c
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-(3-methyl-1H-indol-1-yl)propanoic acid (Fragment 3)
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-(3-methylindol-1-yl)propanoic acid / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 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

Downloads & links

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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)53,0406
Polymers52,4313
Non-polymers6103
Water6,756375
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)106,08112
Polymers104,8616
Non-polymers1,2196
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13210 Å2
ΔGint-100 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.027, 125.115, 118.658
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-413-

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)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-9F8 / 3-(3-methylindol-1-yl)propanoic acid


Mass: 203.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM 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: 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: 1.64→64.97 Å / Num. obs: 69151 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
1.64-1.96.70.4870.9410.2040.528
3.28-64.976.50.0290.9990.0120.032

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Processing

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

5o06


Resolution: 1.642→64.97 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.51
RfactorNum. reflection% reflection
Rfree0.2088 3504 5.07 %
Rwork0.1884 --
obs0.1895 69102 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.65 Å2 / Biso mean: 27.4897 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.642→64.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 45 375 3915
Biso mean--34.6 35.87 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063632
X-RAY DIFFRACTIONf_angle_d0.9764937
X-RAY DIFFRACTIONf_chiral_restr0.038580
X-RAY DIFFRACTIONf_plane_restr0.005641
X-RAY DIFFRACTIONf_dihedral_angle_d12.111301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6422-1.66470.28241700.261425592729
1.6647-1.68850.25671270.244725792706
1.6885-1.71370.25561590.23125892748
1.7137-1.74050.2681430.228526272770
1.7405-1.7690.28381260.23125652691
1.769-1.79950.29051450.225825982743
1.7995-1.83220.25261310.220926452776
1.8322-1.86750.25441490.216525472696
1.8675-1.90560.25141560.210926062762
1.9056-1.9470.28521180.211626112729
1.947-1.99230.26011200.199126322752
1.9923-2.04220.21731290.195526342763
2.0422-2.09740.22971550.18925952750
2.0974-2.15910.19791280.196426122740
2.1591-2.22880.19371330.181726212754
2.2288-2.30850.22641310.179926212752
2.3085-2.40090.19781750.189525992774
2.4009-2.51020.20721440.197126142758
2.5102-2.64250.24061510.19626082759
2.6425-2.80810.20731460.193726422788
2.8081-3.02490.20011120.19326762788
3.0249-3.32930.21581550.196626362791
3.3293-3.8110.18341230.174126812804
3.811-4.80120.15251260.153427102836
4.8012-65.0230.19381520.17927912943

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