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- PDB-3x1k: crystal structure of Phosphoapantetheine adenylyltransferase PPAT... -

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Basic information

Entry
Database: PDB / ID: 3x1k
Titlecrystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with AMP-PNP from Pseudomonas aerugonosa
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / FORMIC ACID / PHOSPHATE ION / Phosphopantetheine adenylyltransferase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa 2192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.547 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 20, 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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,71038
Polymers106,7736
Non-polymers4,93832
Water2,108117
1
A: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,79518
Polymers53,3863
Non-polymers2,40915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-5 kcal/mol
Surface area21750 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,91520
Polymers53,3863
Non-polymers2,52917
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-30 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.325, 89.787, 80.315
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 17795.473 Da / Num. of mol.: 6
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, 149 molecules

#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 20% PEG4000, 0.1M HEPES, 5% Isopropanol, 200mM Sodium acetate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 73 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9748 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.547→39.745 Å / Num. all: 37216 / Num. obs: 36472 / % possible obs: 98 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.55-2.75198
2.75-3.02199.5
3.02-3.46198.5
3.46-4.36198
4.36-50194

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 2.547→39.745 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 2012 5.52 %
Rwork0.1901 --
obs0.1932 36458 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.547→39.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7432 0 290 117 7839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097900
X-RAY DIFFRACTIONf_angle_d1.33710717
X-RAY DIFFRACTIONf_dihedral_angle_d20.4372904
X-RAY DIFFRACTIONf_chiral_restr0.0611199
X-RAY DIFFRACTIONf_plane_restr0.0091352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.547-2.6110.36521460.26042478X-RAY DIFFRACTION98
2.611-2.68160.30961420.23532482X-RAY DIFFRACTION100
2.6816-2.76050.2811470.23622470X-RAY DIFFRACTION99
2.7605-2.84960.28721450.22772456X-RAY DIFFRACTION99
2.8496-2.95140.31551420.22192453X-RAY DIFFRACTION99
2.9514-3.06950.26761470.21512475X-RAY DIFFRACTION99
3.0695-3.20920.26831430.20622490X-RAY DIFFRACTION99
3.2092-3.37830.23621420.19432435X-RAY DIFFRACTION99
3.3783-3.58980.25341460.19032441X-RAY DIFFRACTION98
3.5898-3.86680.23611420.18212477X-RAY DIFFRACTION98
3.8668-4.25550.20621420.16832455X-RAY DIFFRACTION98
4.2555-4.87030.18231350.1632434X-RAY DIFFRACTION97
4.8703-6.13250.27751460.18592456X-RAY DIFFRACTION97
6.1325-39.74980.19681470.1512444X-RAY DIFFRACTION95

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