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- PDB-8zn3: Structure of Phosphopantetheine adenylyltransferase (PPAT) from E... -

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Basic information

Entry
Database: PDB / ID: 8zn3
TitleStructure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter sp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.41 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: 2.41 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 2.41 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: 8I8O
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
Water9,350519
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 area3400 Å2
ΔGint-34 kcal/mol
Surface area16290 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-24 kcal/mol
Surface area15380 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 area3580 Å2
ΔGint-28 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.692, 78.682, 106.902
Angle α, β, γ (deg.)90.000, 93.077, 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.: 519 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
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: 2.41→106.75 Å / Num. obs: 41591 / % possible obs: 94.4 % / Redundancy: 2.2 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.194 / Net I/σ(I): 4.8
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4006 / CC1/2: 0.391 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→106.748 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: FREE R-VALUE / ESU R: 0.603 / ESU R Free: 0.302
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2627 2078 4.996 %
Rwork0.2086 39513 -
all0.211 --
obs-41591 93.804 %
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: 46.791 Å2
Baniso -1Baniso -2Baniso -3
1-1.303 Å2-0 Å20.11 Å2
2--1.58 Å2-0 Å2
3----2.879 Å2
Refinement stepCycle: LAST / Resolution: 2.41→106.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7662 0 68 519 8249
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_deg1.3751.82710770
X-RAY DIFFRACTIONr_angle_other_deg0.7391.74617629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.371551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.347101399
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.40510342
X-RAY DIFFRACTIONr_chiral_restr0.0610.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029219
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021769
X-RAY DIFFRACTIONr_nbd_refined0.2080.21789
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.27310
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23893
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2425
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.259
X-RAY DIFFRACTIONr_nbd_other0.2410.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.226
X-RAY DIFFRACTIONr_mcbond_it3.5284.7673955
X-RAY DIFFRACTIONr_mcbond_other3.5284.7673955
X-RAY DIFFRACTIONr_mcangle_it5.8578.5474944
X-RAY DIFFRACTIONr_mcangle_other5.8578.5484945
X-RAY DIFFRACTIONr_scbond_it3.7225.2674007
X-RAY DIFFRACTIONr_scbond_other3.7225.2674008
X-RAY DIFFRACTIONr_scangle_it6.3169.4725822
X-RAY DIFFRACTIONr_scangle_other6.3159.4725823
X-RAY DIFFRACTIONr_lrange_it10.29553.4018986
X-RAY DIFFRACTIONr_lrange_other10.29753.4188979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.4710.3471220.3372555X-RAY DIFFRACTION82.8793
2.471-2.5380.3611330.3372944X-RAY DIFFRACTION96.7002
2.538-2.6120.3461400.3292828X-RAY DIFFRACTION96.0207
2.612-2.6920.3251520.3012714X-RAY DIFFRACTION96.6937
2.692-2.7810.3011480.2592629X-RAY DIFFRACTION95.3313
2.781-2.8780.3121490.2742591X-RAY DIFFRACTION96.1404
2.878-2.9870.311030.2352467X-RAY DIFFRACTION95.3264
2.987-3.1080.3111260.2392410X-RAY DIFFRACTION96.536
3.108-3.2470.3021310.2212280X-RAY DIFFRACTION95.2212
3.247-3.4050.302990.2182141X-RAY DIFFRACTION92.9461
3.405-3.5890.2581070.2042100X-RAY DIFFRACTION95.9983
3.589-3.8060.228840.181954X-RAY DIFFRACTION93.9604
3.806-4.0690.221060.1731816X-RAY DIFFRACTION94.8667
4.069-4.3940.2471110.1661676X-RAY DIFFRACTION93.4623
4.394-4.8130.229870.1531533X-RAY DIFFRACTION93.9675
4.813-5.3790.19940.1461406X-RAY DIFFRACTION93.3416
5.379-6.2090.265600.1621245X-RAY DIFFRACTION92.161
6.209-7.5980.17590.1321039X-RAY DIFFRACTION91.6528
7.598-10.7180.187370.116775X-RAY DIFFRACTION86.5672
10.718-106.7480.256300.233410X-RAY DIFFRACTION80.5861

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