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- PDB-7kdo: Crystal structure of Escherichia coli HPPK in complex with bisubs... -

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Basic information

Entry
Database: PDB / ID: 7kdo
TitleCrystal structure of Escherichia coli HPPK in complex with bisubstrate inhibitor HP-73
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/INHIBITOR / alpha beta / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
Similarity search - Domain/homology
Chem-H73 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsShaw, G.X. / Shi, G. / Ji, X.
Citation
Journal: Bioorg.Med.Chem. / Year: 2021
Title: Bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: Transition state analogs for high affinity binding.
Authors: Shi, G. / Shaw, G.X. / Zhu, F. / Tarasov, S.G. / 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. / Subburamann, 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.
#4: 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.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,6392
Polymers17,9671
Non-polymers6731
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 70.091, 36.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin- ...6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK


Mass: 17966.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: folK, b0142, JW0138 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.88 Å3/Da / Density % sol: 34.41 % / Mosaicity: 1.526 ° / Mosaicity esd: 0.014 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 27, 2015 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 17716 / % possible obs: 95.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.074 / Χ2: 0.982 / Net I/σ(I): 9.6 / Num. measured all: 88152
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.663.10.58113990.4130.3490.6820.84777.1
1.66-1.723.60.55616220.6220.3130.6420.89589.3
1.72-1.84.10.48417510.7180.2590.5520.9197.2
1.8-1.94.50.38918010.8710.1980.4380.99998
1.9-2.024.80.26217800.9410.1280.2931.00597.9
2.02-2.175.10.18117910.9740.0850.21.00998.4
2.17-2.395.30.12318340.990.0570.1361.00299.2
2.39-2.745.70.08618550.9950.0380.0940.99699.5
2.74-3.456.20.06518790.9970.0270.071.00499.8
3.45-306.40.03120040.9990.0130.0341.00499.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
PHENIX1.7.3phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UDV

3udv


Resolution: 1.6→29.93 Å / SU ML: 0.1917 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1000 5.65 %
Rwork0.1842 16689 -
obs0.1865 17689 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 47 170 1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861365
X-RAY DIFFRACTIONf_angle_d1.03271870
X-RAY DIFFRACTIONf_chiral_restr0.0546205
X-RAY DIFFRACTIONf_plane_restr0.0056241
X-RAY DIFFRACTIONf_dihedral_angle_d15.9554508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.32221170.28231936X-RAY DIFFRACTION79.82
1.68-1.790.29121380.26612324X-RAY DIFFRACTION94.69
1.79-1.930.30161460.23732415X-RAY DIFFRACTION98.09
1.93-2.120.24451440.19132417X-RAY DIFFRACTION97.9
2.12-2.430.23061470.16882456X-RAY DIFFRACTION99.12
2.43-3.060.21261500.1722504X-RAY DIFFRACTION99.66
3.06-29.930.19051580.16362637X-RAY DIFFRACTION100

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