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

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Basic information

Entry
Database: PDB / ID: 1dy3
TitleTernary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsPYROPHOSPHORYLASE / DE NOVO FOLATE BIOSYNTHESIS
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-87Y / ADENOSINE-5'-TRIPHOSPHATE / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
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.
History
DepositionJan 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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)18,8365
Polymers17,9671
Non-polymers8694
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
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-MC2221

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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) / Gene: folK, b0142, JW0138 / 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 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / 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 / Source method: obtained synthetically / Formula: C16H19N5O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common 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: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: R-AXIS / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 10879 / % possible obs: 94.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 10.6 / Rsym value: 0.102 / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 47660 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 92.2 % / Rmerge(I) obs: 0.102

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.165 --
obs-10829 94.9 %
Displacement parametersBiso mean: 19.7 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 56 141 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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