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- PDB-6j3m: Crystal structure of the complex of Phosphopantetheine adenylyltr... -

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Basic information

Entry
Database: PDB / ID: 6j3m
TitleCrystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Pyrophosphate at 2.30A 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
PYROPHOSPHATE 2- / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSingh, P.K. / Gupta, A. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Pyrophosphate at 2.30A resolution
Authors: Singh, P.K. / Gupta, A. / Sharma, S. / Singh, T.P.
History
DepositionJan 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: 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
Item: _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)18,8225
Polymers18,4791
Non-polymers3434
Water1,60389
1
A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,46615
Polymers55,4373
Non-polymers1,02912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation82_555-y,z,-x1
Buried area5490 Å2
ΔGint-93 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.120, 216.120, 216.120
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, pantetheine-phosphate adenylyltransferase
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: 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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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: 78.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97199 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2018 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 2.3→76.41 Å / Num. obs: 19784 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.16 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1898 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZZC

5zzc


Resolution: 2.3→76.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.278 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21914 1010 5.1 %RANDOM
Rwork0.18569 ---
obs0.1875 18770 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.693 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→76.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 16 89 1410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131347
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171239
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.6451825
X-RAY DIFFRACTIONr_angle_other_deg1.4421.572860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08521.68877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.67515224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4091510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021500
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_it5.5474.479651
X-RAY DIFFRACTIONr_mcbond_other5.4674.471650
X-RAY DIFFRACTIONr_mcangle_it8.1166.696812
X-RAY DIFFRACTIONr_mcangle_other8.1156.708813
X-RAY DIFFRACTIONr_scbond_it7.7885.576696
X-RAY DIFFRACTIONr_scbond_other7.5545.553685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.1987.932995
X-RAY DIFFRACTIONr_long_range_B_refined13.96354.7041507
X-RAY DIFFRACTIONr_long_range_B_other13.98754.2441488
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
Rfree0.258 63 -
Rwork0.248 1374 -
obs--100 %

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