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- PDB-4ruk: crystal structure of Phosphoapantetheine adenylyltransferase PPAT... -

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Basic information

Entry
Database: PDB / ID: 4ruk
Titlecrystal structure of Phosphoapantetheine adenylyltransferase PPAT/CoaD with CoA and pyrophosphate 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
ACETATE ION / COENZYME A / FORMIC ACID / PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa 2192 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: RCSB / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)113,53245
Polymers106,7736
Non-polymers6,75939
Water2,522140
1
A: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,82723
Polymers53,3863
Non-polymers3,44120
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15180 Å2
ΔGint-31 kcal/mol
Surface area21350 Å2
MethodPISA
2
B: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70522
Polymers53,3863
Non-polymers3,31819
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14750 Å2
ΔGint-30 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.603, 89.483, 79.616
Angle α, β, γ (deg.)90.00, 97.93, 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) / 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 , 8 types, 179 molecules

#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG4000, 0.1M HEPES, 5% Isopropanol, 200mM Sodium aceate, pH 7.0, 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: 2.2→45.132 Å / Num. all: 77595 / Num. obs: 54318 / % possible obs: 71 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.25171
2.25-2.31183
2.31-2.37197
2.37-2.44199.5
2.44-2.52199.8
2.52-2.61199.6
2.61-2.71199.8
2.71-2.84199.8
2.84-2.99199.8
2.99-3.17199.9
3.17-3.42199.9
3.42-3.761100
3.76-4.311100
4.31-5.42199.8
5.42-50199.9

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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: 2.2→45.132 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 1999 3.68 %
Rwork0.2042 --
obs0.2061 54318 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7456 0 411 140 8007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098183
X-RAY DIFFRACTIONf_angle_d1.26211101
X-RAY DIFFRACTIONf_dihedral_angle_d17.413060
X-RAY DIFFRACTIONf_chiral_restr0.0521222
X-RAY DIFFRACTIONf_plane_restr0.0061383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25520.37391030.32622756X-RAY DIFFRACTION71
2.2552-2.31610.33711270.28333241X-RAY DIFFRACTION85
2.3161-2.38430.36511460.2633772X-RAY DIFFRACTION98
2.3843-2.46120.30131440.24193824X-RAY DIFFRACTION99
2.4612-2.54920.2811500.23243848X-RAY DIFFRACTION100
2.5492-2.65130.28921490.21873858X-RAY DIFFRACTION100
2.6513-2.77190.28891430.19763829X-RAY DIFFRACTION100
2.7719-2.9180.25711440.1993874X-RAY DIFFRACTION100
2.918-3.10080.24181450.20783827X-RAY DIFFRACTION100
3.1008-3.34010.2811510.20053896X-RAY DIFFRACTION100
3.3401-3.67610.26141490.19253847X-RAY DIFFRACTION100
3.6761-4.20780.24161470.19053895X-RAY DIFFRACTION100
4.2078-5.30.22381530.18423894X-RAY DIFFRACTION100
5.3-45.14180.2061480.19913958X-RAY DIFFRACTION100

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