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- PDB-5yrr: The crystal structure of Phosphopantetheine adenylyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 5yrr
TitleThe crystal structure of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.88 A resolution
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE
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
COENZYME A / Phosphopantetheine adenylyltransferase / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsBairagya, H.R. / Gupta, A. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: The crystal structure of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.88 A resolution
Authors: Bairagya, H.R. / Gupta, A. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)19,5355
Polymers18,4791
Non-polymers1,0564
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-30 kcal/mol
Surface area9370 Å2
Unit cell
Length a, b, c (Å)216.260, 216.260, 216.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#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 (bacteria) / Gene: coaD / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059ZFC5, UniProt: B0VTH7*PLUS, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 5.7 Å3/Da / Density % sol: 78.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.88→65.2 Å / Num. obs: 10184 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 2.88→2.933 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / Num. unique obs: 501

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YH7

5yh7


Resolution: 2.88→65.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.883 / SU B: 15.539 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27857 485 4.8 %RANDOM
Rwork0.22594 ---
obs0.22839 9698 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.541 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.88→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 63 21 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191401
X-RAY DIFFRACTIONr_bond_other_d0.0050.021270
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9871903
X-RAY DIFFRACTIONr_angle_other_deg1.50732935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7085162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05223.52968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.95715226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2621510
X-RAY DIFFRACTIONr_chiral_restr0.2620.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021517
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02306
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_it5.0645.199651
X-RAY DIFFRACTIONr_mcbond_other5.0145.193650
X-RAY DIFFRACTIONr_mcangle_it7.9167.8812
X-RAY DIFFRACTIONr_mcangle_other7.9217.81813
X-RAY DIFFRACTIONr_scbond_it5.1495.948750
X-RAY DIFFRACTIONr_scbond_other5.1475.961739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0948.8071074
X-RAY DIFFRACTIONr_long_range_B_refined12.58399.7425537
X-RAY DIFFRACTIONr_long_range_B_other12.58299.7555532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.883→2.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 35 -
Rwork0.427 700 -
obs--99.59 %

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