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- PDB-4nau: S. aureus CoaD with Inhibitor -

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Basic information

Entry
Database: PDB / ID: 4nau
TitleS. aureus CoaD with Inhibitor
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTransferase/transferase inhibitor / Phosphopanthetheine Adenylyltransferase / CoaBC / Transferase-transferase inhibitor complex
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
Chem-2W3 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLahiri, S.D.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Discovery of Inhibitors of 4'-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy.
Authors: de Jonge, B.L. / Walkup, G.K. / Lahiri, S.D. / Huynh, H. / Neckermann, G. / Utley, L. / Nash, T.J. / Brock, J. / San Martin, M. / Kutschke, A. / Johnstone, M. / Laganas, V. / Hajec, L. / Gu, ...Authors: de Jonge, B.L. / Walkup, G.K. / Lahiri, S.D. / Huynh, H. / Neckermann, G. / Utley, L. / Nash, T.J. / Brock, J. / San Martin, M. / Kutschke, A. / Johnstone, M. / Laganas, V. / Hajec, L. / Gu, R.F. / Ni, H. / Chen, B. / Hutchings, K. / Holt, E. / McKinney, D. / Gao, N. / Livchak, S. / Thresher, J.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)57,3077
Polymers55,1913
Non-polymers2,1154
Water1,26170
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,61314
Polymers110,3836
Non-polymers4,2308
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21570 Å2
ΔGint-100 kcal/mol
Surface area39990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.095, 127.782, 127.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 18397.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: coaD, MW1007 / Production host: Escherichia coli (E. coli)
References: UniProt: P63820, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-2W3 / 2-[2-[(1S,2S)-2-[(3,4-dichlorophenyl)methylcarbamoyl]cyclohexyl]-6-ethyl-pyrimidin-4-yl]-4-oxidanyl-6-oxidanylidene-1H-pyrimidine-5-carboxamide


Mass: 545.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26Cl2N6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% to 19% polyethylene glycol 3350 (PEG 3350), 200 mM ammonium sulfate, 0.1M Propionic acid Cacodylate Bis-tris propane buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.33→31.94 Å / Num. obs: 26990 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.33→2.386 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.4.0066refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→31.94 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.797 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32043 1354 5 %RANDOM
Rwork0.25611 ---
obs0.25943 25636 98.78 %-
all-13456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.33→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 130 70 4062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194073
X-RAY DIFFRACTIONr_bond_other_d0.0010.023852
X-RAY DIFFRACTIONr_angle_refined_deg1.8392.0085510
X-RAY DIFFRACTIONr_angle_other_deg0.90438912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63124.237177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34715753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3561521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2944.3651913
X-RAY DIFFRACTIONr_mcbond_other2.2944.3651912
X-RAY DIFFRACTIONr_mcangle_it3.1966.5462386
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8974.5732160
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 81 -
Rwork0.324 1576 -
obs--84.33 %

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