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- PDB-4pzv: Crystal structure of Francisella tularensis HPPK-DHPS in complex ... -

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Basic information

Entry
Database: PDB / ID: 4pzv
TitleCrystal structure of Francisella tularensis HPPK-DHPS in complex with bisubstrate analog HPPK inhibitor J1D
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
KeywordsTRANSFERASE / Ferredoxin-like fold / TIM barrel fold / ATP binding / Phosphorylation
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 / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme ...7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 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. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J1D / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 Å
AuthorsShaw, G.X. / Shi, G. / Ji, X.
Citation
Journal: Febs J. / Year: 2014
Title: Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis.
Authors: Shaw, G.X. / Li, Y. / Shi, G. / Wu, Y. / Cherry, S. / Needle, D. / Zhang, D. / Tropea, J.E. / Waugh, D.S. / Yan, H. / Ji, X.
#1: Journal: J.Med.Chem. / Year: 2001
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H.
#2: Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
Authors: Shi, G. / Shaw, G. / Liang, Y.H. / Subburaman, P. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
#3: Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: new lead exhibits a distinct binding mode.
Authors: Shi, G. / Shaw, G. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,3839
Polymers48,3141
Non-polymers1,0698
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.945, 74.434, 69.758
Angle α, β, γ (deg.)90.000, 93.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48313.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: foIK, folK, FTT_0942c / Plasmid: pDN2163 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q5NGA7, dihydropteroate synthase, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-J1D / 5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine


Mass: 634.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N12O8S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG monomethyl ether 2000, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2012 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 43013 / Num. obs: 43013 / % possible obs: 90 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.001 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.761.90.4051.934160.99972.1
1.76-1.832.20.3812.138530.95580.9
1.83-1.912.50.3812.340201.00584.9
1.91-2.022.90.3552.742211.00388.9
2.02-2.143.30.3123.544571.00692.8
2.14-2.313.50.2434.544410.99993.5
2.31-2.543.70.19645181.00394.5
2.54-2.9140.133945721.00495.5
2.91-3.664.80.06519.746971.00498
3.66-305.20.03441.448181.00599

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
Blu-Ice5data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3UDE and 1TWS

3ude

1tws


Resolution: 1.704→28.106 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 979 2.28 %Random
Rwork0.2104 ---
all0.2145 43002 --
obs0.2115 43002 89.74 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.3 Å2 / Biso mean: 18.4151 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: LAST / Resolution: 1.704→28.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 72 430 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093665
X-RAY DIFFRACTIONf_angle_d1.0754957
X-RAY DIFFRACTIONf_chiral_restr0.062560
X-RAY DIFFRACTIONf_plane_restr0.005636
X-RAY DIFFRACTIONf_dihedral_angle_d12.5191444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.704-1.79380.38431030.359747924895489572
1.7938-1.90620.37171300.328455815711571184
1.9062-2.05330.31211270.266759726099609989
2.0533-2.25990.27481430.22362176360636093
2.2599-2.58670.27891600.191362816441644194
2.5867-3.25820.22821500.180864606610661096
3.2582-28.11010.20921660.164467206886688699

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