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- PDB-8sl9: Crystal structure of Francisella tularensis HPPK-DHPS in complex ... -

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Basic information

Entry
Database: PDB / ID: 8sl9
TitleCrystal structure of Francisella tularensis HPPK-DHPS in complex with HPPK inhibitor HP-73
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE / Francisella tularensis / HPPK-DHPS / bisubstrate inhibitor / HP-73
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / dihydropteroate synthase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
Chem-H73 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsShaw, G.X. / Shi, G. / Cherry, S. / Needle, D. / Tropea, J.E. / Waugh, D.S. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of Francisella tularensis HPPK-DHPS in complex with HPPK inhibitor HP-73
Authors: Shaw, G.X. / Shi, G. / Cherry, S. / Needle, D. / Tropea, J.E. / Waugh, D.S. / Ji, X.
History
DepositionApr 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57227
Polymers48,4281
Non-polymers2,14526
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Francisella tularensis HPPK-DHPS in complex with bisubstrate inhibitor HP-101
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.847, 73.977, 69.557
Angle α, β, γ (deg.)90.00, 94.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase


Mass: 48427.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: folK / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NGA7
#2: Chemical ChemComp-H73 / 5'-S-[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]-5'-thioadenosine


Mass: 672.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N12O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, NaCl, etc.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020 / Details: Si(111)
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 82829 / % possible obs: 97.8 % / Redundancy: 3.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.044 / Rrim(I) all: 0.088 / Χ2: 0.954 / Net I/σ(I): 13.6 / Num. measured all: 313011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.452.91.03181450.3910.750.7011.2550.95996.5
1.45-1.513.10.8180320.480.8050.5330.9760.96695.3
1.51-1.583.90.64283160.7090.9110.3780.7481.01698.5
1.58-1.6640.44583210.8420.9560.260.5171.04198.7
1.66-1.763.90.28883250.9130.9770.1690.3351.03498.5
1.76-1.93.80.17183450.9640.9910.1030.2010.95998.6
1.9-2.093.70.09680810.9860.9970.0590.1130.89495.8
2.09-2.394.20.06884430.9940.9980.0380.0780.94299.2
2.39-3.024.20.05183980.9960.9990.0290.0590.89398.9
3.02-3040.03884230.9970.9990.0210.0430.84297.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→28.1 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 1003 1.21 %Random selection
Rwork0.1641 ---
obs0.1642 82755 97.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 138 371 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0243775
X-RAY DIFFRACTIONf_angle_d1.7755076
X-RAY DIFFRACTIONf_dihedral_angle_d13.9431462
X-RAY DIFFRACTIONf_chiral_restr0.126574
X-RAY DIFFRACTIONf_plane_restr0.012644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.470.29441330.288911109X-RAY DIFFRACTION93
1.47-1.570.27471450.225911638X-RAY DIFFRACTION98
1.57-1.690.23091530.197211793X-RAY DIFFRACTION99
1.69-1.860.19751380.173811841X-RAY DIFFRACTION99
1.86-2.130.1831400.154711558X-RAY DIFFRACTION97
2.13-2.680.17191470.148711912X-RAY DIFFRACTION99
2.68-28.10.14061470.145911901X-RAY DIFFRACTION98

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