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- PDB-8zn2: Structure of Phosphopantetheine adenylyltransferase (PPAT) from E... -

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Basic information

Entry
Database: PDB / ID: 8zn2
TitleStructure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.65 A resolution.
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / coaD / PPAT / COENZYME A biosynthesis
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
PHOSPHONOACETIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEnterobacter sp. 638 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsAhmad, N. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchI-1251 India
CitationJournal: To Be Published
Title: Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.65 A resolution.
Authors: Ahmad, N. / Sharma, P. / Bhushan, A. / Sharma, S. / Singh, T.P.
History
DepositionMay 25, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 5, 2024ID: 8I8M
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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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)116,24216
Polymers115,0946
Non-polymers1,14910
Water9,332518
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7375
Polymers38,3652
Non-polymers3723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-33 kcal/mol
Surface area16240 Å2
MethodPISA
2
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7996
Polymers38,3652
Non-polymers4344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-25 kcal/mol
Surface area15360 Å2
MethodPISA
3
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7075
Polymers38,3652
Non-polymers3423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-28 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.929, 78.643, 107.005
Angle α, β, γ (deg.)90.000, 93.117, 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: 19182.268 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-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.74 %
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: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.651→42.64 Å / Num. obs: 31523 / % possible obs: 94.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5
Reflection shellResolution: 2.651→2.697 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1555 / CC1/2: 0.842 / % possible all: 96.3

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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: 2.651→42.64 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: FREE R-VALUE / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2345 1535 4.869 %
Rwork0.1705 29988 -
all0.173 --
obs-31523 94.42 %
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: 44.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.708 Å20 Å20.325 Å2
2--1.196 Å2-0 Å2
3----2.922 Å2
Refinement stepCycle: LAST / Resolution: 2.651→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7662 0 68 518 8248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127962
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167655
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.82710770
X-RAY DIFFRACTIONr_angle_other_deg0.741.74617629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.729551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.194101399
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.76410342
X-RAY DIFFRACTIONr_chiral_restr0.0620.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029219
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021769
X-RAY DIFFRACTIONr_nbd_refined0.2080.21758
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.27136
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23878
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2419
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.249
X-RAY DIFFRACTIONr_nbd_other0.2680.2195
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.21
X-RAY DIFFRACTIONr_mcbond_it3.464.4983955
X-RAY DIFFRACTIONr_mcbond_other3.464.4983955
X-RAY DIFFRACTIONr_mcangle_it5.6668.0654944
X-RAY DIFFRACTIONr_mcangle_other5.6668.0654945
X-RAY DIFFRACTIONr_scbond_it3.8824.9964007
X-RAY DIFFRACTIONr_scbond_other3.8824.9964008
X-RAY DIFFRACTIONr_scangle_it6.4658.9725822
X-RAY DIFFRACTIONr_scangle_other6.4658.9725823
X-RAY DIFFRACTIONr_lrange_it10.12449.0948911
X-RAY DIFFRACTIONr_lrange_other10.12649.1078905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.651-2.720.3211130.2562232X-RAY DIFFRACTION96.1854
2.72-2.7940.2631180.2252174X-RAY DIFFRACTION96.3025
2.794-2.8740.2951120.2052096X-RAY DIFFRACTION96
2.874-2.9630.2761120.1992042X-RAY DIFFRACTION94.9735
2.963-3.0590.2651320.2121962X-RAY DIFFRACTION95.2251
3.059-3.1660.223970.1841929X-RAY DIFFRACTION95.8826
3.166-3.2850.279910.1831845X-RAY DIFFRACTION96.1749
3.285-3.4180.236910.1991817X-RAY DIFFRACTION95.7831
3.418-3.5690.294940.1871714X-RAY DIFFRACTION95.7627
3.569-3.7420.214770.1621639X-RAY DIFFRACTION95.6522
3.742-3.9430.2041040.1521540X-RAY DIFFRACTION94.974
3.943-4.180.22640.1491468X-RAY DIFFRACTION93.7576
4.18-4.4650.199640.1351359X-RAY DIFFRACTION93.3727
4.465-4.8180.189550.1241266X-RAY DIFFRACTION93.3569
4.818-5.2720.221490.1491181X-RAY DIFFRACTION90.6411
5.272-5.8830.209400.1631039X-RAY DIFFRACTION91.3633
5.883-6.7710.23470.156935X-RAY DIFFRACTION91.4339
6.771-8.2410.238250.146798X-RAY DIFFRACTION90.5391
8.241-11.4440.142350.115610X-RAY DIFFRACTION88.7208
11.444-42.640.306140.246342X-RAY DIFFRACTION81.0934

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