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- PDB-5yh7: Crystal structure of the complex of Phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 5yh7
TitleCrystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.0 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
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSingh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii.
Authors: Gupta, A. / Singh, P.K. / Iqbal, N. / Sharma, P. / Baraigya, H.R. / Kaur, P. / Umar, M.S. / Ahmad, F. / Sharma, A. / Owais, M. / Sharma, S. / Singh, T.P.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.2Nov 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

Downloads & links

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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
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.930, 216.930, 216.930
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 (strain ACICU) (bacteria)
Strain: ACICU / Gene: coaD, ACICU_00798 / Production host: Escherichia coli (E. coli)
References: UniProt: B2HUN5, 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.: 70 / 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: 5.6 Å3/Da / Density % sol: 78.63 %
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
PH range: 5-8

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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
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2→125.24 Å / Num. obs: 24872 / % possible obs: 88.1 % / Redundancy: 8.3 % / Rsym value: 0.072 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.39 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 2.03→125.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.546 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21497 1269 5 %RANDOM
Rwork0.19812 ---
obs0.19896 24053 88.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.271 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.03→125.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 63 70 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0191397
X-RAY DIFFRACTIONr_bond_other_d0.0030.021268
X-RAY DIFFRACTIONr_angle_refined_deg2.8131.9871898
X-RAY DIFFRACTIONr_angle_other_deg1.35832928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7875162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26323.43367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.42615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.2931510
X-RAY DIFFRACTIONr_chiral_restr0.20.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021513
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02306
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_it6.1294.663651
X-RAY DIFFRACTIONr_mcbond_other6.0734.659650
X-RAY DIFFRACTIONr_mcangle_it8.2156.965812
X-RAY DIFFRACTIONr_mcangle_other8.2266.972813
X-RAY DIFFRACTIONr_scbond_it8.2375.637746
X-RAY DIFFRACTIONr_scbond_other8.2335.639735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.468.1811069
X-RAY DIFFRACTIONr_long_range_B_refined13.41590.3465551
X-RAY DIFFRACTIONr_long_range_B_other13.41490.3375552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.032→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 21 -
Rwork0.379 441 -
obs--22.38 %

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