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- PDB-3nd6: Crystal structure of phosphopantetheine adenylyltransferase (PPAT... -

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Basic information

Entry
Database: PDB / ID: 3nd6
TitleCrystal structure of phosphopantetheine adenylyltransferase (PPAT) in complex with ATP from Enterococcus faecalis
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Phosphopantetheine adenylyltransferase / PPAT / Coenzyme A biosynthetic pathway
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
ADENOSINE-5'-TRIPHOSPHATE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYoon, H.J. / Lee, H.H. / Suh, S.W.
CitationJournal: Mol.Cells / Year: 2011
Title: Crystal structure of phosphopantetheine adenylyltransferase from Enterococcus faecalis in the ligand-unbound state and in complex with ATP and pantetheine
Authors: Yoon, H.J. / Kang, J.Y. / Mikami, B. / Lee, H.H. / Suh, S.W.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)121,66712
Polymers118,6246
Non-polymers3,0436
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-89 kcal/mol
Surface area38540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.793, 123.906, 124.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19770.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: coaD / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q831P9, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.5M sodium formate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2006 / Details: Mirrors
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 76960 / % possible obs: 98.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.7 / Num. measured all: 534418
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 10.9 / Num. unique all: 7489 / % possible all: 97.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VLH

1vlh


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 7607 -RANDOM
Rwork0.206 ---
obs-75428 97 %-
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 186 413 7943

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