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

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Basic information

Entry
Database: PDB / ID: 3pxu
TitleCrystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei bound to dephospho-coenzyme A
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / HUMAN AND ANIMAL PATHOGEN / MELIOIDOSIS / ATP-BINDING / COENZYME A BIOSYNTHESIS / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / PPAT / pantetheine-phosphate adenylyltransferase
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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionDec 22, 2010ID: 3IKZ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Oct 30, 2013Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 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

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Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9146
Polymers18,8501
Non-polymers1,0645
Water1,60389
1
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)119,48136
Polymers113,0986
Non-polymers6,38330
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 area26570 Å2
ΔGint-323 kcal/mol
Surface area36460 Å2
MethodPISA
2
A: Phosphopantetheine adenylyltransferase
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)477,924144
Polymers452,39224
Non-polymers25,533120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area102890 Å2
ΔGint-1254 kcal/mol
Surface area149220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.161, 134.161, 134.161
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

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Components

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


Mass: 18849.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0748, coaD, coaD BURPS1710B_0748 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JW91, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Hampton Crystal Screen condition c8, 2.0 M ammonium sulfate, 5.5 mg/mL protein with expression tag removed, crystal tracking ID 203611c8, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 13128 / % possible obs: 99 % / Redundancy: 23.2 % / Rmerge(I) obs: 0.087 / Χ2: 1.097 / Net I/σ(I): 44.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.1822.40.5196.5711811.11698.1
2.18-2.2628.70.4211.111971.114100
2.26-2.3729.20.36512.312191.137100
2.37-2.4929.30.29114.912091.106100
2.49-2.6529.30.2418.712251.104100
2.65-2.8529.40.16127.712091.165100
2.85-3.1429.40.10540.312371.059100
3.14-3.5929.30.07256.412361.047100
3.59-4.5228.90.0466112670.921100
4.52-5027.20.03290.713471.21399.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.6 Å
Translation2.5 Å28.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6T molecule A, protein only

1b6t


Resolution: 2.1→28.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2172 / WRfactor Rwork: 0.1847 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8339 / SU B: 9.406 / SU ML: 0.114 / SU R Cruickshank DPI: 0.2065 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 620 5 %RANDOM
Rwork0.1995 ---
obs0.2016 12286 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.24 Å2 / Biso mean: 29.9984 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 66 89 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221345
X-RAY DIFFRACTIONr_angle_refined_deg1.4632.0161825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60722.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50415221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1061512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021979
X-RAY DIFFRACTIONr_mcbond_it0.8541.5804
X-RAY DIFFRACTIONr_mcangle_it1.54921296
X-RAY DIFFRACTIONr_scbond_it2.5843541
X-RAY DIFFRACTIONr_scangle_it4.2574.5526
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 42 -
Rwork0.205 827 -
all-869 -
obs--97.42 %
Refinement TLS params.Method: refined / Origin x: -20.3175 Å / Origin y: 40.5112 Å / Origin z: -14.7962 Å
111213212223313233
T0.0587 Å20.0089 Å2-0.0036 Å2-0.0399 Å20.0207 Å2--0.0151 Å2
L1.2644 °2-0.1648 °2-0.1582 °2-0.2716 °2-0.037 °2--0.3621 °2
S-0.0766 Å °-0.0051 Å °0.0373 Å °0.0184 Å °0.0516 Å °0.0013 Å °-0.0097 Å °0.0254 Å °0.025 Å °

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