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- PDB-5jbn: Crystal Structure of Apo Phosphopantetheine Adenylyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 5jbn
TitleCrystal Structure of Apo Phosphopantetheine Adenylyltransferase (PPAT/CoaD) from E. coli
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / CoaD / Apo / PPAT
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / identical protein 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
Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsMamo, M. / Proudfoot, A. / Bussiere, D.
CitationJournal: J.Biomol.Nmr / Year: 2016
Title: Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids.
Authors: Proudfoot, A. / Frank, A.O. / Ruggiu, F. / Mamo, M. / Lingel, A.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1479
Polymers38,4922
Non-polymers6557
Water6,359353
1
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules

A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,44027
Polymers115,4776
Non-polymers1,96421
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_467z-1,-x+1,-y+21
crystal symmetry operation12_676-y+1,-z+2,x+11
Buried area19590 Å2
ΔGint-420 kcal/mol
Surface area36310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.176, 136.176, 136.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Phosphopantetheine adenylyltransferase / Dephospho-CoA pyrophosphorylase / Pantetheine-phosphate adenylyltransferase / PPAT


Mass: 19246.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaD, kdtB, yicA, b3634, JW3609 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6I6, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.8 M ammonium sulfate, 0.25 M potassium thiocyanate, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→39.32 Å / Num. obs: 74142 / % possible obs: 99.5 % / Redundancy: 19.4 % / Net I/σ(I): 41.4
Reflection shellHighest resolution: 1.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 1.45→36.395 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.36
RfactorNum. reflection% reflection
Rfree0.1823 3758 4.99 %
Rwork0.1451 --
obs0.1469 74015 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→36.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 34 353 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062691
X-RAY DIFFRACTIONf_angle_d0.7913668
X-RAY DIFFRACTIONf_dihedral_angle_d23.867981
X-RAY DIFFRACTIONf_chiral_restr0.072414
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4423-1.46060.25061360.21722665X-RAY DIFFRACTION100
1.4606-1.47980.2721130.20922628X-RAY DIFFRACTION100
1.4798-1.50010.24461510.19722636X-RAY DIFFRACTION100
1.5001-1.52150.2151370.18022600X-RAY DIFFRACTION100
1.5215-1.54420.24161270.17312669X-RAY DIFFRACTION100
1.5442-1.56830.20211240.16442656X-RAY DIFFRACTION100
1.5683-1.59410.17071530.16532634X-RAY DIFFRACTION100
1.5941-1.62150.20191260.1542606X-RAY DIFFRACTION100
1.6215-1.6510.21181440.15172622X-RAY DIFFRACTION100
1.651-1.68280.16971500.15612633X-RAY DIFFRACTION100
1.6828-1.71710.19491350.15052631X-RAY DIFFRACTION100
1.7171-1.75450.18571570.14392622X-RAY DIFFRACTION100
1.7545-1.79530.16891390.13972610X-RAY DIFFRACTION100
1.7953-1.84020.18631400.13792649X-RAY DIFFRACTION100
1.8402-1.88990.1591400.13472647X-RAY DIFFRACTION100
1.8899-1.94550.18291360.13532639X-RAY DIFFRACTION100
1.9455-2.00830.15251510.13362635X-RAY DIFFRACTION100
2.0083-2.08010.16841570.13832624X-RAY DIFFRACTION100
2.0801-2.16340.17811290.13792629X-RAY DIFFRACTION100
2.1634-2.26180.1911340.13452680X-RAY DIFFRACTION100
2.2618-2.38110.16681610.13562620X-RAY DIFFRACTION100
2.3811-2.53020.17971370.13782656X-RAY DIFFRACTION100
2.5302-2.72550.16071400.14412676X-RAY DIFFRACTION100
2.7255-2.99970.17721630.14172625X-RAY DIFFRACTION100
2.9997-3.43340.18751190.14012709X-RAY DIFFRACTION100
3.4334-4.32470.20021200.1312704X-RAY DIFFRACTION100
4.3247-36.40610.17541390.16522789X-RAY DIFFRACTION100

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