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- PDB-8i8p: Crystal structure of the complex of phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 8i8p
TitleCrystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 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
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsAhmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution.
Authors: Ahmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 4, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 12, 2023ID: 6KYG
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)19,4186
Polymers18,4791
Non-polymers9395
Water1,60389
1
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,83712
Polymers36,9582
Non-polymers1,87910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation85_544y+1/4,x-1/4,-z-1/41
Buried area6070 Å2
ΔGint-122 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.038, 217.038, 217.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18479.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Gene: coaD, HMPREF0010_01342
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D0C9M9, pantetheine-phosphate adenylyltransferase

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.76 Å3/Da / Density % sol: 78.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 2.19→125.307 Å / Num. obs: 22090 / % possible obs: 95.48 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 16.2
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 1044 / CC1/2: 0.631

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→125.307 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 1044 4.726 %
Rwork0.2011 21046 -
all0.203 --
obs-22090 95.582 %
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: 63.419 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.19→125.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 56 89 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121391
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161296
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.651886
X-RAY DIFFRACTIONr_angle_other_deg1.1051.5712970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.226512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.3451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1710224
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.6351067
X-RAY DIFFRACTIONr_chiral_restr0.0950.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021605
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02340
X-RAY DIFFRACTIONr_nbd_refined0.2220.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.21190
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2699
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2920.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.218
X-RAY DIFFRACTIONr_nbd_other0.2960.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.216
X-RAY DIFFRACTIONr_mcbond_it6.4556.008651
X-RAY DIFFRACTIONr_mcbond_other6.4496.011651
X-RAY DIFFRACTIONr_mcangle_it8.76410.786812
X-RAY DIFFRACTIONr_mcangle_other8.80210.789813
X-RAY DIFFRACTIONr_scbond_it9.3997.33740
X-RAY DIFFRACTIONr_scbond_other9.3377.306733
X-RAY DIFFRACTIONr_scangle_it13.61212.9621074
X-RAY DIFFRACTIONr_scangle_other13.61112.9251063
X-RAY DIFFRACTIONr_lrange_it15.80665.6491622
X-RAY DIFFRACTIONr_lrange_other15.65264.5771593
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
2.19-2.2470.369640.34510060.34716720.9250.91263.99520.332
2.247-2.3090.423570.32812100.33216390.8990.92677.30320.306
2.309-2.3760.421740.31614600.32115790.9090.93897.15010.282
2.376-2.4490.312660.30714740.30715400.9430.9471000.269
2.449-2.5290.306720.28514180.28614900.9450.9581000.239
2.529-2.6180.309510.26313950.26414460.9550.9611000.214
2.618-2.7170.288610.25313350.25513960.9590.9681000.211
2.717-2.8270.229800.20912730.2113530.9660.9731000.178
2.827-2.9530.291530.21912530.22213060.9520.9691000.195
2.953-3.0970.345520.23411930.23812450.9180.9651000.214
3.097-3.2640.296560.2311320.23311880.9430.9691000.217
3.264-3.4620.287480.21610800.21811280.9550.9761000.211
3.462-3.7010.284550.21610130.21910680.9590.9781000.219
3.701-3.9970.233580.1959440.19710020.970.981000.206
3.997-4.3790.168450.1638830.1639280.9840.9861000.189
4.379-4.8950.14430.1258070.1268500.9840.991000.151
4.895-5.650.191330.1777290.1787620.9870.9821000.217
5.65-6.9170.304320.2066180.2116500.9520.9761000.249
6.917-9.7670.173340.1454960.1475310.9840.98899.81170.201
9.767-125.3070.245100.2413270.2413380.9760.95199.70410.403

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