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- PDB-3x1m: Crystal structure of Phosphopantetheine adenylyltransferase/PPAT ... -

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Basic information

Entry
Database: PDB / ID: 3x1m
TitleCrystal structure of Phosphopantetheine adenylyltransferase/PPAT from Pseudomonas aeruginosa with CoA
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Rossmann Fold Transferase
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
ACETATE ION / COENZYME A / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Phosphopantetheine adenylyltransferase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa 2192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,89622
Polymers53,3863
Non-polymers3,50919
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-37 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.810, 120.490, 89.750
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) / 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, 102 molecules

#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 295 K / pH: 7.2
Details: 16% PEG4000, 0.1M HEPES, 200mM Sodium acetate, 5% Isopropanol, pH 7.2, 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
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.5→45.25 Å / Num. obs: 20201 / % possible obs: 99 % / Observed criterion σ(I): 1.8
Reflection shellResolution: 2.5→45.33 Å / % possible all: 99.9

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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: 2.5→45.25 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1019 5.1 %
Rwork0.196 --
obs0.199 19999 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 216 83 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114056
X-RAY DIFFRACTIONf_angle_d1.4715496
X-RAY DIFFRACTIONf_dihedral_angle_d17.031508
X-RAY DIFFRACTIONf_chiral_restr0.061607
X-RAY DIFFRACTIONf_plane_restr0.007697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63190.35981360.26262669X-RAY DIFFRACTION100
2.6319-2.79670.30671380.23742677X-RAY DIFFRACTION100
2.7967-3.01260.34881480.22752679X-RAY DIFFRACTION100
3.0126-3.31570.25321580.21112681X-RAY DIFFRACTION100
3.3157-3.79530.25471440.19022708X-RAY DIFFRACTION100
3.7953-4.78080.22941430.1642733X-RAY DIFFRACTION100
4.7808-45.26260.21841520.18522833X-RAY DIFFRACTION100

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