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- PDB-3f3m: Six Crystal Structures of Two Phosphopantetheine Adenylyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3f3m
TitleSix Crystal Structures of Two Phosphopantetheine Adenylyltransferases Reveal an Alternative Ligand Binding Mode and an Associated Structural Change
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Phosphopantetheine adenylyltransferase / PPAT / Coenzyme A biosynthetic pathway / Coenzyme A biosynthesis / Nucleotidyltransferase
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
3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLee, H.H. / Yoon, H.J. / Suh, S.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode
Authors: Lee, H.H. / Yoon, H.J. / Kang, J.Y. / Park, J.H. / Kim, D.J. / Choi, K.H. / Lee, S.K. / Song, J. / Kim, H.J. / Suh, S.W.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: 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

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9762
Polymers19,4681
Non-polymers5071
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.774, 66.774, 124.134
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 19468.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: coaD / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: P63820, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM imidazone, 0.9-1.2M potassium/sodium tartrate, 0.2M NaCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2004 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 12227 / % possible obs: 98.8 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1161 / % possible all: 93.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B6T

1b6t


Resolution: 2.4→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.25 1217 9.9 %
Rwork0.211 --
obs-6328 96.2 %
Solvent computationBsol: 34.131 Å2
Displacement parametersBiso max: 95.89 Å2 / Biso mean: 31.96 Å2 / Biso min: 5.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.958 Å2-2.876 Å20 Å2
2---2.958 Å20 Å2
3---5.915 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 31 43 1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9811.5
X-RAY DIFFRACTIONc_scbond_it2.9732
X-RAY DIFFRACTIONc_mcangle_it3.1782
X-RAY DIFFRACTIONc_scangle_it3.9852.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3atp.param

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