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- PDB-4mb2: Crystal structure of TON1374 in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4mb2
TitleCrystal structure of TON1374 in complex with ATP
ComponentsPhosphopantothenate synthetase
KeywordsLIGASE / ATP binding
Function / homology
Function and homology information


4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding
Similarity search - Function
Phosphopantoate/pantothenate synthetase / Phosphopantoate/pantothenate synthetase / Phosphopantoate/pantothenate synthetase superfamily / Phosphopantothenate/pantothenate synthetase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4-phosphopantoate--beta-alanine ligase
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsKim, M.-K. / An, Y.J. / Cha, S.-S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1
Authors: Kim, M.-K. / An, Y.J. / Cha, S.-S.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Phosphopantothenate synthetase
B: Phosphopantothenate synthetase
C: Phosphopantothenate synthetase
D: Phosphopantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9839
Polymers118,9304
Non-polymers2,0535
Water3,225179
1
A: Phosphopantothenate synthetase
B: Phosphopantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5045
Polymers59,4652
Non-polymers1,0393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-43 kcal/mol
Surface area20960 Å2
MethodPISA
2
C: Phosphopantothenate synthetase
D: Phosphopantothenate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4794
Polymers59,4652
Non-polymers1,0142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-24 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.428, 60.909, 75.241
Angle α, β, γ (deg.)90.00, 92.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phosphopantothenate synthetase / Putative uncharacterized protein


Mass: 29732.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_1374 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YXQ1, EC: 6.3.2.26
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 0.08M Tris-HCl, 24%(w/v) polyethylene glycol 4000, 4mM ATP, pH 8.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 60918 / Num. obs: 60918 / % possible obs: 97.8 % / Observed criterion σ(I): 4.8
Reflection shellResolution: 2.19→2.23 Å / % possible all: 92.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→37.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.318 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 3084 5.1 %RANDOM
Rwork0.2013 ---
obs0.2043 57833 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.19 Å2 / Biso mean: 48.6026 Å2 / Biso min: 11.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å22.67 Å2
2--0.59 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.19→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8021 0 125 179 8325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198270
X-RAY DIFFRACTIONr_bond_other_d00.028245
X-RAY DIFFRACTIONr_angle_refined_deg1.0832.00711184
X-RAY DIFFRACTIONr_angle_other_deg0.567318918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93951003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18623.154371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.922151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8051592
X-RAY DIFFRACTIONr_chiral_restr0.0670.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0219054
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021766
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 219 -
Rwork0.33 4073 -
all-4292 -
obs--93.49 %

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