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

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Basic information

Entry
Database: PDB / ID: 7kdr
TitleCrystal structure of Escherichia coli HPPK in complex with bisubstrate inhibitor HP-75
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 / 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-J1L / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.488 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8315
Polymers17,9671
Non-polymers8644
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.446, 42.797, 56.283
Angle α, β, γ (deg.)90.000, 101.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-454-

HOH

31A-557-

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-J1L / 5'-{[(2R,4R)-1-{2-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)amino]ethyl}-2-carboxypiperidin-4-yl]sulfonyl}-5'-deoxyadenosine


Mass: 704.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N12O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.02 Å3/Da / Density % sol: 39.04 % / Mosaicity: 1.498 ° / Mosaicity esd: 0.017 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG-8000

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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: Feb 20, 2020
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 22571 / % possible obs: 94.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.053 / Rrim(I) all: 0.134 / Χ2: 0.88 / Net I/σ(I): 12.4 / Num. measured all: 122333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.532.60.32515030.8750.2010.3850.84864.3
1.53-1.593.90.3222670.90.170.3640.86395.5
1.59-1.6750.30223220.9270.1450.3360.93997.9
1.67-1.755.40.26423360.9460.1220.2920.91198.7
1.75-1.865.50.23523780.9560.1080.260.98498.9
1.86-2.015.30.20122730.9610.0940.2230.70295.9
2.01-2.216.10.17923440.9750.0770.1950.78998.7
2.21-2.536.60.16423620.9760.0680.1770.91999.1
2.53-3.196.50.12723770.9870.0540.1380.92299
3.19-306.30.09524090.9860.0410.1040.87697.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KDO

7kdo


Resolution: 1.488→28.971 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1000 4.45 %
Rwork0.1624 21492 -
obs0.1641 22492 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.03 Å2 / Biso mean: 25.4774 Å2 / Biso min: 8.74 Å2
Refinement stepCycle: final / Resolution: 1.488→28.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 105 268 1640
Biso mean--30.36 40.62 -
Num. residues----158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4882-1.56670.26621180.2301252679
1.5667-1.66490.22321440.2051310298
1.6649-1.79340.23531490.1783318999
1.7934-1.97380.22261440.1773309296
1.9738-2.25930.21811450.1584312598
2.2593-2.84610.19511500.1581322599
2.8461-28.9710.17831500.149323398

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