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- PDB-6an4: Crystal structure of Escherichia coli HPPK in complex with bisubs... -

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Basic information

Entry
Database: PDB / ID: 6an4
TitleCrystal structure of Escherichia coli HPPK in complex with bisubstrate analogue inhibitor HP-39 (J1F)
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/INHIBITOR / alpha beta / 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 / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J1F / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.47 Å
AuthorsShaw, G.X. / Shi, G. / Ji, X.
Citation
Journal: to be published
Title: Bisubstrate analog inhibitors of HPPK: Transition state mimetics
Authors: Shaw, X.G. / Shi, 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 designnnnn 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: Shi, G. / Shaw, G. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
History
DepositionAug 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
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

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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)18,6963
Polymers17,9671
Non-polymers7292
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-5 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.778, 48.092, 77.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Fragment: Full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: folK, b0142, JW0138 / Plasmid: pDN2163 / Production host: Escherichia coli / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-J1F / ((2-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carboxamido)-N-(2-((((2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)acetamido)methyl)phosphonic acid / 5'-{[N-(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridine-6-carbonyl)glycyl-N-(phosphonomethyl)glycyl]amino}-5'-deoxyadenosine


Mass: 693.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N13O10P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.26 Å3/Da / Density % sol: 45.5 % / Mosaicity: 0.293 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NaCl, sodium citrate etc.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 21, 2014 / 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: 1.45→30 Å / Num. obs: 27163 / % possible obs: 91.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 18.36 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.019 / Rrim(I) all: 0.046 / Χ2: 0.917 / Net I/σ(I): 11.7 / Num. measured all: 149656
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.530.3115310.920.1830.3630.71952.8
1.5-1.563.70.31721700.9140.1780.3660.70774.6
1.56-1.634.80.30227260.9550.150.3390.71693.8
1.63-1.725.80.26629200.9810.1190.2920.77299.7
1.72-1.836.10.18329160.9910.080.20.902100
1.83-1.976.10.11429480.9940.050.1240.993100
1.97-2.176.10.07529460.9960.0330.0821.005100
2.17-2.486.10.05629670.9970.0250.0620.993100
2.48-3.1260.03630100.9990.0160.0391.00499.9
3.12-305.80.02730290.9990.0120.030.99595.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.47→29.846 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 980 3.69 %Random selection
Rwork0.2 ---
obs0.2003 26578 93.69 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å
Displacement parametersBiso max: 85.36 Å2 / Biso mean: 25.9825 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.47→29.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 79 227 1510
Biso mean--25.22 31.06 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051421
X-RAY DIFFRACTIONf_angle_d0.9211959
X-RAY DIFFRACTIONf_chiral_restr0.061215
X-RAY DIFFRACTIONf_plane_restr0.004258
X-RAY DIFFRACTIONf_dihedral_angle_d14.953538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.54750.2985970.26012527262466
1.5475-1.64450.27021350.24423557369292
1.6445-1.77150.24251480.23938363984100
1.7715-1.94970.26311470.219138634010100
1.9497-2.23170.24531500.208238974047100
2.2317-2.81140.20781500.193639414091100
2.8114-29.85190.17771530.18393977413097

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