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- PDB-5o06: Crystal structure of APO form of Phosphopantetheine adenylyltrans... -

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Basic information

Entry
Database: PDB / ID: 5o06
TitleCrystal structure of APO form of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus
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
Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.547 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)52,5555
Polymers52,4313
Non-polymers1242
Water5,134285
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)105,11010
Polymers104,8616
Non-polymers2484
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14290 Å2
ΔGint-85 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.867, 124.503, 118.567
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-293-

HOH

21C-332-

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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM Sodium fluoride 20% PEG3350 0.1MBis-Tris propane pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→56.85 Å / Num. obs: 79696 / % possible obs: 97.2 % / Redundancy: 8.3 % / Biso Wilson estimate: 22.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.012 / Rrim(I) all: 0.036 / Net I/σ(I): 28.4 / Num. measured all: 660031 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.635.70.51266709116220.9030.2270.5632.698.5
4.89-56.858.40.01823411277810.0060.01997.299.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RHS

3rhs


Resolution: 1.547→56.853 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 3949 4.96 %
Rwork0.1979 75650 -
obs0.1987 79599 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.27 Å2 / Biso mean: 28.8765 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 1.547→56.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 8 285 3817
Biso mean--32.14 35.26 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063633
X-RAY DIFFRACTIONf_angle_d0.9714941
X-RAY DIFFRACTIONf_chiral_restr0.038587
X-RAY DIFFRACTIONf_plane_restr0.005646
X-RAY DIFFRACTIONf_dihedral_angle_d12.0121306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5466-1.56550.33711500.27182631278196
1.5655-1.58530.25851610.25512678283997
1.5853-1.60620.28771460.24792693283999
1.6062-1.62820.29981260.234727582884100
1.6282-1.65140.26671390.239927792918100
1.6514-1.67610.25061400.223127542894100
1.6761-1.70230.25481540.212627432897100
1.7023-1.73020.2251290.211127722901100
1.7302-1.760.26251590.216427412900100
1.76-1.7920.25621520.215727352887100
1.792-1.82650.23951660.205827722938100
1.8265-1.86380.25831530.199327302883100
1.8638-1.90430.26271470.205927602907100
1.9043-1.94860.2541960.21212101219776
1.9486-1.99730.18921660.202927432909100
1.9973-2.05130.20011210.195128092930100
2.0513-2.11170.2057970.19822244234180
2.1117-2.17990.24961290.199427752904100
2.1799-2.25780.21651310.20172377250886
2.2578-2.34820.20151420.200528272969100
2.3482-2.4550.21961490.205127442893100
2.455-2.58450.25491380.212628142952100
2.5845-2.74640.24171050.208928242929100
2.7464-2.95840.23781830.209727802963100
2.9584-3.25610.21081440.207428072951100
3.2561-3.72720.20651220.18622549267190
3.7272-4.69560.18431460.16452760290696
4.6956-56.89120.16681580.188129503108100

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