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- PDB-6a6d: Crystal structure of the complex of Phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 6a6d
TitleCrystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.90A 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
DEPHOSPHO COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSingh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.90A resolution
Authors: Singh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJun 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: 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)19,2874
Polymers18,4791
Non-polymers8083
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.479, 216.479, 216.479
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-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H35N7O13P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 78.53 %
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: 4-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 14, 2018 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.9→48.41 Å / Num. obs: 9622 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.99 / Rrim(I) all: 0.105 / Net I/σ(I): 26.7
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 15 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 2466 / Rrim(I) all: 0.99 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YH7

5yh7


Resolution: 2.9→44.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.826 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24138 507 5 %RANDOM
Rwork0.17685 ---
obs0.18023 9622 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.9→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 50 23 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0141387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171230
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.6991884
X-RAY DIFFRACTIONr_angle_other_deg1.0531.662874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99521.66778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.03415225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4951510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021540
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02281
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_it9.1248.608651
X-RAY DIFFRACTIONr_mcbond_other9.128.599650
X-RAY DIFFRACTIONr_mcangle_it12.92612.906812
X-RAY DIFFRACTIONr_mcangle_other12.9212.917813
X-RAY DIFFRACTIONr_scbond_it11.65110.079734
X-RAY DIFFRACTIONr_scbond_other11.64810.097731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.97114.7181066
X-RAY DIFFRACTIONr_long_range_B_refined20.9471557
X-RAY DIFFRACTIONr_long_range_B_other20.9851554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å
RfactorNum. reflection% reflection
Rfree0.45 36 -
Rwork0.35 679 -
obs--100 %

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