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- PDB-6jog: Crystal structure of the complex of phospho pantetheine adenylyl ... -

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Basic information

Entry
Database: PDB / ID: 6jog
TitleCrystal structure of the complex of phospho pantetheine adenylyl transferase from Acinetobacter baumannii with two ascorbic acid (Vitamin-C) molecules.
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
ASCORBIC ACID / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsViswanathan, V. / Gupta, A. / Bairagya, H.R. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of phospho pantetheine adenylyl transferase from Acinetobacter baumannii with two ascorbic acid (Vitamin-C) molecules.
Authors: Viswanathan, V. / Gupta, A. / Bairagya, H.R. / Sharma, S. / Singh, T.P.
History
DepositionMar 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,9274
Polymers18,4791
Non-polymers4483
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint0 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.667, 216.667, 216.667
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


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, pantetheine-phosphate adenylyltransferase
#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 5.73 Å3/Da / Density % sol: 78.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
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: 2.3→125.1 Å / Num. obs: 19945 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.96 / Rrim(I) all: 0.12 / Net I/σ(I): 14.65
Reflection shellResolution: 2.3→2.36 Å / Mean I/σ(I) obs: 3.76 / Num. unique obs: 3474 / CC1/2: 0.82 / Rrim(I) all: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
REFMAC5.8.0238phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZZC

5zzc


Resolution: 2.3→125.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.206 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.22572 1025 5.1 %RANDOM
Rwork0.19305 ---
obs0.19466 18920 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.199 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→125.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 29 88 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131363
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171247
X-RAY DIFFRACTIONr_angle_refined_deg2.221.661846
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5812882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61521.68877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.03115224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3061510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
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_it5.745.036651
X-RAY DIFFRACTIONr_mcbond_other5.6545.033650
X-RAY DIFFRACTIONr_mcangle_it7.7917.547812
X-RAY DIFFRACTIONr_mcangle_other7.8077.553813
X-RAY DIFFRACTIONr_scbond_it8.6456.215712
X-RAY DIFFRACTIONr_scbond_other8.4676.196705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.7568.8971027
X-RAY DIFFRACTIONr_long_range_B_refined13.55661.3451498
X-RAY DIFFRACTIONr_long_range_B_other13.5661.3491497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 70 -
Rwork0.3 1359 -
obs--100 %

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