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- PDB-5o0f: Crystal structure of Phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 5o0f
TitleCrystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-(indol-3-yl)propanoic acid (Fragment 5)
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
INDOLYLPROPIONIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus ATCC 19977 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 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)52,8095
Polymers52,4313
Non-polymers3782
Water6,612367
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)105,61810
Polymers104,8616
Non-polymers7574
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area16360 Å2
ΔGint-79 kcal/mol
Surface area35270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.073, 125.239, 118.460
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-298-

HOH

21C-302-

HOH

31C-345-

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 ATCC 19977 (bacteria)
Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-IOP / INDOLYLPROPIONIC ACID


Mass: 189.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 200mM Sodium bromide 20-25% PEG 3350 0.1M Bis-Tris propane
PH range: 6.5 to 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: 1.7→59.23 Å / Num. obs: 61858 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 23.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.9713.50.5530.9680.1550.57499.6
3.41-59.2312.60.0330.9990.010.03499.9

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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: 1.704→59.23 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2305 3049 4.93 %
Rwork0.2018 --
obs0.2032 61804 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.66 Å2 / Biso mean: 30.0091 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 1.704→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 28 367 3890
Biso mean--35.5 38.49 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073622
X-RAY DIFFRACTIONf_angle_d1.0164917
X-RAY DIFFRACTIONf_chiral_restr0.042576
X-RAY DIFFRACTIONf_plane_restr0.004642
X-RAY DIFFRACTIONf_dihedral_angle_d12.8581300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7037-1.73030.30631390.26792602274199
1.7303-1.75870.29791320.263526802812100
1.7587-1.7890.29961260.25282619274599
1.789-1.82160.27471080.24932659276799
1.8216-1.85660.34091400.23892649278999
1.8566-1.89450.27021530.229626132766100
1.8945-1.93570.28431300.22562659278999
1.9357-1.98070.2731410.221326502791100
1.9807-2.03030.3021410.222126362777100
2.0303-2.08520.24241230.213226522775100
2.0852-2.14650.23971690.206226372806100
2.1465-2.21580.23071520.200426502802100
2.2158-2.2950.23641630.197126312794100
2.295-2.38690.23141440.207126592803100
2.3869-2.49550.22591320.209126612793100
2.4955-2.62710.24941300.214527182848100
2.6271-2.79170.27241120.210826902802100
2.7917-3.00720.2241290.208927002829100
3.0072-3.30980.23851270.205227282855100
3.3098-3.78870.21661660.194926792845100
3.7887-4.77310.20071540.157927272881100
4.7731-59.26580.18581380.197628562994100

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