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- PDB-3udv: Crystal structure of E. coli HPPK in complex with bisubstrate ana... -

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Basic information

Entry
Database: PDB / ID: 3udv
TitleCrystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1C
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Alpha Beta / Kinase / ATP Binding / Pyrophosphoryl Transfer / 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 / 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
ACETATE ION / Chem-J1C / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 Å
AuthorsShaw, G. / Shi, G. / Ji, X.
Citation
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.
#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.
History
DepositionOct 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: 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 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)18,6543
Polymers17,9671
Non-polymers6882
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.00, 70.64, 36.25
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 (E. coli) / Strain: K12 / Gene: b0142, foIK, folK, JW0138 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-J1C / 5'-S-[1-(2-{[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]amino}ethyl)piperidin-4-yl]-5'-thioadenosine


Mass: 628.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36N12O5S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, ammonium acetate, Bis-Tris, pH 7.5, vapor diffusion, sitting drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 13, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→30 Å / Num. all: 11716 / Num. obs: 11716 / % possible obs: 87.6 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.074 / Χ2: 0.981 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.852.80.3226580.967150.4
1.85-1.933.70.3278640.955166
1.93-2.024.70.28810270.976178.1
2.02-2.125.60.24511740.959189.1
2.12-2.266.20.21212291.042194.2
2.26-2.436.60.1612840.975196.5
2.43-2.677.10.13913140.971199.8
2.67-3.067.20.09513540.9991100
3.06-3.857.10.0513550.9811100
3.85-306.60.03514570.959199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 3UDE

3ude


Resolution: 1.88→29.921 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.48 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 920 8.55 %Random
Rwork0.2099 ---
obs0.2155 10754 92.78 %-
all-10754 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.371 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 87.68 Å2 / Biso mean: 27.3913 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.88→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 48 91 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131365
X-RAY DIFFRACTIONf_angle_d1.3761876
X-RAY DIFFRACTIONf_chiral_restr0.087208
X-RAY DIFFRACTIONf_plane_restr0.008242
X-RAY DIFFRACTIONf_dihedral_angle_d14.998531
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 (%)
1.88-1.97910.2881980.252810521150115072
1.9791-2.10310.36641190.26312651384138486
2.1031-2.26540.34421310.256514131544154494
2.2654-2.49330.29761360.226314501586158697
2.4933-2.85380.29291400.2063149616361636100
2.8538-3.59450.26011450.1873154716921692100
3.5945-29.92460.23311510.1926161117621762100

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