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- PDB-3x1j: Crystal Structure of Phosphopantetheine adenylyltransferase (PPAT... -

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Basic information

Entry
Database: PDB / ID: 3x1j
TitleCrystal Structure of Phosphopantetheine adenylyltransferase (PPAT/CoaD) with AcCoA from Pseudomonas aeruginosa
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Rossmann Fold
Function / homology
Function and homology information


[citrate (pro-3S)-lyase] ligase activity / pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Citrate lyase ligase, C-terminal / Citrate lyase ligase C-terminal domain / 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
ACETYL COENZYME *A / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphopantetheine adenylyltransferase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa 2192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.334 Å
AuthorsChatterjee, R. / Datta, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Transition of phosphopantetheine adenylyltransferase from catalytic to allosteric state is characterized by ternary complex formation in Pseudomonas aeruginosa
Authors: Chatterjee, R. / Mondal, A. / Basu, A. / Datta, S.
History
DepositionNov 19, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Data collection
Revision 1.2May 4, 2016Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)56,92019
Polymers53,3863
Non-polymers3,53416
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-20 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.900, 120.700, 90.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase


Mass: 17795.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 2192 (bacteria) / Strain: 2192 / Gene: coaD, PA0363, PA2G_04277 / Production host: Escherichia coli (E. coli)
References: UniProt: A3LHH1, UniProt: A0A0X1KGP2*PLUS, pantetheine-phosphate adenylyltransferase

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Non-polymers , 6 types, 53 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 53.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG4000 18%, 0.1M HEPES, 5% Isopropanol, 200mM Sodium acetate., pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9748 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.334→45.328 Å / Num. obs: 24934 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8
Reflection shellResolution: 2.33→2.47 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.334→45.328 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1257 5.1 %
Rwork0.226 --
obs0.228 24666 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.334→45.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 214 37 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014020
X-RAY DIFFRACTIONf_angle_d1.65448
X-RAY DIFFRACTIONf_dihedral_angle_d17.3051499
X-RAY DIFFRACTIONf_chiral_restr0.063603
X-RAY DIFFRACTIONf_plane_restr0.01678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.334-2.42740.33151210.28382589X-RAY DIFFRACTION100
2.4274-2.53790.34761530.26792528X-RAY DIFFRACTION100
2.5379-2.67170.30781340.25012593X-RAY DIFFRACTION100
2.6717-2.83910.30691480.23772561X-RAY DIFFRACTION100
2.8391-3.05820.2781540.242565X-RAY DIFFRACTION100
3.0582-3.36590.33251340.22762599X-RAY DIFFRACTION100
3.3659-3.85270.27961490.22572599X-RAY DIFFRACTION100
3.8527-4.85320.22731390.20242624X-RAY DIFFRACTION100
4.8532-45.33620.25071250.20542751X-RAY DIFFRACTION100

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