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- PDB-1eq0: SOLUTION STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSP... -

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Basic information

Entry
Database: PDB / ID: 1eq0
TitleSOLUTION STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH MGAMPPCP
Components6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE
KeywordsTRANSFERASE / FOLATE PTERIN / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / INDUCED CONFORMATIONAL CHANGE
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
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry simulated annealing
Model type detailsminimized average
AuthorsShi, G. / Yan, H.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.
Authors: Xiao, B. / Shi, G. / Gao, J. / Blaszczyk, J. / Liu, Q. / Ji, X. / Yan, H.
#1: Journal: J.BIOMOL.NMR / Year: 1999
Title: 1H, 13C and 15N Resonance Assignments of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin Pyrophosphokinase and its Complex with MgAMPPCP
Authors: Shi, G. / Gao, J. / Yan, H.
#2: Journal: Structure / Year: 1999
Title: Crystal Structure of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, a Potential Target for the Development of Novel Antimicrobial Agents.
Authors: Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X.
History
DepositionMar 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE


Theoretical massNumber of molelcules
Total (without water)17,9671
Polymers17,9671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN 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) / Plasmid: pET-17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.5mM HPPK U-15N,13C; 20mM phosphate buffer A; 90% H2O, 10% D2O N
Solvent system: 0% H2O, 10% D2O
Sample conditionspH: 7.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.9Brungerrefinement
NMRPipeNIHdata analysis
VNMR6.1Variancollection
NMRView4.1Merckdata analysis
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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