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- PDB-3k9w: Crystal structure of phosphopantetheine adenylyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 3k9w
TitleCrystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei with hydrolyzed 3'-dephospho Coenzyme A
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Coenzyme A / CoA / biosynthesis / hydrolysis / ATP-binding / Coenzyme A biosynthesis / Nucleotide-binding / Nucleotidyltransferase
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
4'-diphospho pantetheine / ACETATE ION / ADENINE / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei.
Authors: Edwards, T.E. / Leibly, D.J. / Bhandari, J. / Statnekov, J.B. / Phan, I. / Dieterich, S.H. / Abendroth, J. / Staker, B.L. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J.
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Oct 30, 2013Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)21,7646
Polymers20,8411
Non-polymers9235
Water2,468137
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)130,58236
Polymers125,0456
Non-polymers5,53730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation37_454y-1/2,x+1/2,-z-1/21
crystal symmetry operation42_454-x-1/2,z+1/2,y-1/21
crystal symmetry operation48_454-z-1/2,-y+1/2,-x-1/21
Buried area24420 Å2
ΔGint-163 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.431, 134.431, 134.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 20840.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: coaD, BURPS1710b_0748 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JW91, pantetheine-phosphate adenylyltransferase

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Non-polymers , 6 types, 142 molecules

#2: Chemical ChemComp-4PS / 4'-diphospho pantetheine / N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 438.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24N2O10P2S
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COD/COA IN THE STRUCTURE APPEARS TO BE HYDROLYZED ACCORDING TO THE ELECTRON DENSITY WITH ...THE COD/COA IN THE STRUCTURE APPEARS TO BE HYDROLYZED ACCORDING TO THE ELECTRON DENSITY WITH DIFFRACTION LIMITS OF 1.6 ANGSTROM. ONE COMPONENT IS 4'-DIPHOSPHO PANTETHEINE DENOTED AS 4PS IN THE COORDINATES. THE OTHER COMPONENTS ARE DEFINED AS ADENINE (ADE), SULFATE (SO4) AND THREE WATERS, WHICH FITS WELL INTO THE ELECTRON DENSITY MAP. THIS MODEL BEST REPRESENTS WHAT IS OBSERVED IN THE CRYSTAL.

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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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: CSHT condition F1: 0.2 M ammonium sulfate, 0.1 M NaOAc pH 4.6, 30% PEG MME 2000, 20% EG as cryo-protectant, 19.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 5 mM DTT, ...Details: CSHT condition F1: 0.2 M ammonium sulfate, 0.1 M NaOAc pH 4.6, 30% PEG MME 2000, 20% EG as cryo-protectant, 19.2 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% glycerol, 5 mM DTT, crystal tracking ID 204963f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97953 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 27383 / % possible obs: 99 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 32.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.98 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IKZ

3ikz
PDB Unreleased entry


Resolution: 1.6→26.36 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.2 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1363 5 %RANDOM
Rwork0.19119 ---
obs0.192 25986 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.125 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 55 137 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9971978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5595186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0923.0366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5271512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211107
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6461.5857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24821395
X-RAY DIFFRACTIONr_scbond_it1.9123596
X-RAY DIFFRACTIONr_scangle_it3.1154.5574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 113 -
Rwork0.266 1905 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -20.6496 Å / Origin y: 40.3354 Å / Origin z: -14.9325 Å
111213212223313233
T0.0218 Å20.0035 Å20.0006 Å2-0.0363 Å20.0032 Å2--0.0062 Å2
L0.815 °2-0.1022 °2-0.2033 °2-0.4859 °20.0567 °2--0.5799 °2
S-0.0412 Å °-0.0208 Å °0.004 Å °0.0163 Å °-0.0082 Å °-0.0143 Å °-0.0144 Å °0.043 Å °0.0494 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 161
2X-RAY DIFFRACTION1A167 - 171
3X-RAY DIFFRACTION1A172 - 308

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