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- PDB-9u54: Structure of Phosphopantetheine adenylyltransferase (PPAT) from E... -

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Basic information

Entry
Database: PDB / ID: 9u54
TitleStructure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the 17-mer expression tag bound in the substrate binding site of a neighbouring molecule at 2.10 A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / coaD / PPAT / COENZYME A biosynthesis / EXPRESSION TAG
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 / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
CITRIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEnterobacter sp. 638 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsAhmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchI-1251 India
CitationJournal: Biochemistry / Year: 2025
Title: Design of Peptide Inhibitors Using Expression Tags: Structure of the Complex of Phosphopantetheine Adenylyltransferase with 17-Residue Expression-Tag Peptide and Citric Acid at 2.10 angstrom Resolution.
Authors: Ahmad, N. / Kumar, V. / Goel, V.K. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionMar 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)117,94012
Polymers116,7876
Non-polymers1,1536
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-121 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.308, 78.676, 106.797
Angle α, β, γ (deg.)90.000, 93.249, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19464.545 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. 638 (bacteria) / Gene: coaD, Ent638_0105 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A4W515, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.1→49.29 Å / Num. obs: 65468 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.109 / Net I/σ(I): 6.2
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 1.438 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4023 / CC1/2: 0.268 / Rpim(I) all: 1.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxCuBEdata collection
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→43.325 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.208 / Average fsc free: 0.9327 / Average fsc work: 0.948 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2775 1302 1.989 %
Rwork0.2238 64159 -
all0.225 --
obs-65461 98.651 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.913 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å2-0 Å2-0.466 Å2
2--0.461 Å2-0 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.101→43.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7702 0 78 472 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127969
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167649
X-RAY DIFFRACTIONr_angle_refined_deg1.411.82110778
X-RAY DIFFRACTIONr_angle_other_deg0.7561.74617606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.897551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.566101396
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.44410339
X-RAY DIFFRACTIONr_chiral_restr0.0620.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029241
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021771
X-RAY DIFFRACTIONr_nbd_refined0.2180.21794
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.27397
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23926
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2447
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2630.245
X-RAY DIFFRACTIONr_nbd_other0.2190.2160
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_mcbond_it3.8435.0363960
X-RAY DIFFRACTIONr_mcbond_other3.845.0363960
X-RAY DIFFRACTIONr_mcangle_it5.9399.0354944
X-RAY DIFFRACTIONr_mcangle_other5.949.0354945
X-RAY DIFFRACTIONr_scbond_it4.2455.5914009
X-RAY DIFFRACTIONr_scbond_other4.2375.5924006
X-RAY DIFFRACTIONr_scangle_it6.89110.0435832
X-RAY DIFFRACTIONr_scangle_other6.89110.0435833
X-RAY DIFFRACTIONr_lrange_it9.94251.8169016
X-RAY DIFFRACTIONr_lrange_other9.94951.5668935
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.101-2.1550.367670.38541750.38548540.8930.87787.39180.38
2.155-2.2140.396890.36646320.36647550.8790.89399.2850.36
2.214-2.2780.36940.32945050.3346260.8890.91199.41630.317
2.278-2.3480.323810.31243750.31244750.920.92899.57540.297
2.348-2.4250.313960.29242360.29343480.9270.93899.6320.274
2.425-2.510.345830.28341190.28442170.9350.94399.64430.265
2.51-2.6040.295740.27239970.27340800.9520.95399.77940.252
2.604-2.710.347920.25938340.26139350.920.95699.77130.239
2.71-2.830.277740.21236630.21437480.9580.9799.70650.192
2.83-2.9680.313730.21434900.21635770.9320.9799.60860.199
2.968-3.1280.351840.2433380.24234290.9130.96699.79590.225
3.128-3.3160.319390.2232150.22232570.9320.97299.90790.212
3.316-3.5440.262510.2329590.23130210.9620.97299.63590.223
3.544-3.8250.246570.20527850.20528540.9660.97799.57950.2
3.825-4.1870.218620.16525570.16626330.9710.98499.46830.163
4.187-4.6760.24490.14123170.14323810.970.98899.370.143
4.676-5.3890.199520.17420410.17521050.9740.98399.42990.177
5.389-6.5750.389270.23317670.23518140.9380.97498.89750.231
6.575-9.1930.228420.17913420.18113970.9770.98399.06940.189
9.193-43.3250.2160.1948120.1948420.9730.97498.33730.211

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