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- PDB-1dy3: Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphoki... -

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Entry
Database: PDB / ID: 1dy3
TitleTernary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.
Components
KeywordsPYROPHOSPHORYLASE / DE NOVO FOLATE BIOSYNTHESIS
Function / homology7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 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 ...7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 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 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Function and homology information
Specimen sourceESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MIR / 2 Å resolution
AuthorsStammers, D.K. / Achari, A. / Somers, D.O. / Bryant, P.K. / Rosemond, J. / Scott, D.L. / Champness, J.N.
CitationJournal: FEBS Lett. / Year: 1999
Title: 2.0A X-Ray Structure of the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase from Escherichia Coli with ATP and a Substrate Analogue
Authors: Stammers, D.K. / Achari, A. / Somers, D.O. / Bryant, P.K. / Rosemond, J. / Scott, D.L. / Champness, J.N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2000 / Release: Aug 18, 2000
RevisionDateData content typeGroupProviderType
1.0Aug 18, 2000Structure modelrepositoryInitial release
1.1May 7, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 700 SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEETS IN THIS STRUCTURE. THIS IS REPRESENTED BY ... SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEETS IN THIS STRUCTURE. THIS IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A:
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8365
Polyers17,9671
Non-polymers8694
Water2,540141
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)40.960, 69.010, 115.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide / PPPK / HPPK


Mass: 17966.535 Da / Num. of mol.: 1 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical ChemComp-87Y / 7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN / 2-AMINO-6-HYDROXYMETHYL-7-METHYL-7-PHENETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE / 7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN


Mass: 313.354 Da / Num. of mol.: 1 / Formula: C16H19N5O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Formula: H2O / Water

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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: 2.27 / Density percent sol: 45.84 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
15 mg/mlPPPK1drop
22 mMdithiothreitol1drop
36 mM1dropMgCl2
40.7 mMATP1drop
50.5 mMpterin1drop
60.1 Msodium citrate1reservoir
70.2 Mammonium acetate1reservoir
827-31 %(w/v)PEG34001reservoir

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Data collection

DiffractionMean temperature: 29
SourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: R-AXIS / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 / Relative weight: 1
ReflectionB iso Wilson estimate: 15.3 / D resolution high: 2 / D resolution low: 4 / Number obs: 10879 / Rsym value: 0.05 / NetI over sigmaI: 20.5 / Redundancy: 4.4 % / Percent possible obs: 94.4
Reflection shellHighest resolution: 2 / Lowest resolution: 2.07 / MeanI over sigI obs: 10.6 / Rsym value: 0.102 / Percent possible all: 92.8
Reflection
*PLUS
Number measured all: 47660 / Rmerge I obs: 0.05
Reflection shell
*PLUS
Percent possible obs: 92.2 / Rmerge I obs: 0.102

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MIR / Sigma F: 0
Displacement parametersB iso mean: 19.7
Least-squares processR factor R work: 0.165 / Highest resolution: 2 / Lowest resolution: 1 / Number reflection obs: 10829 / Percent reflection obs: 94.9
Refine hist #LASTHighest resolution: 2 / Lowest resolution: 1
Number of atoms included #LASTProtein: 1267 / Nucleic acid: 0 / Ligand: 56 / Solvent: 141 / Total: 1464
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.027
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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