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- PDB-1jkn: Solution Structure of the Nudix Enzyme Diadenosine Tetraphosphate... -

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Basic information

Entry
Database: PDB / ID: 1jkn
TitleSolution Structure of the Nudix Enzyme Diadenosine Tetraphosphate Hydrolase from Lupinus angustifolius Complexed with ATP
Componentsdiadenosine 5',5'''-P1,P4-tetraphosphate hydrolase
KeywordsHYDROLASE / alpha-beta-alpha sandwich / enzyme-substrate complex
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / bis(5'-adenosyl)-pentaphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / chloroplast / metal ion binding
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...RNA pyrophosphohydrolase RppH / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase
Similarity search - Component
Biological speciesLupinus angustifolius (narrow-leaved blue lupine)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsFletcher, J.I. / Swarbrick, J.D. / Maksel, D. / Gayler, K.R. / Gooley, P.R.
Citation
Journal: Structure / Year: 2002
Title: The structure of Ap(4)A hydrolase complexed with ATP-MgF(x) reveals the basis of substrate binding.
Authors: Fletcher, J.I. / Swarbrick, J.D. / Maksel, D. / Gayler, K.R. / Gooley, P.R.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: The Three-dimensional Structure of the Nudix Enzyme Diadenosine Tetraphosphate Hydrolase from Lupinus angustifolius L
Authors: Swarbrick, J.D. / Bashtannyk, T. / Maksel, D. / Zhang, X.-R. / Blackburn, G.M. / Gayler, K.R. / Gooley, P.R.
History
DepositionJul 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3412
Polymers18,8341
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with favorable non-bond energy, structures with the least restraint violations, target function
RepresentativeModel #21lowest energy

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Components

#1: Protein diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase


Mass: 18834.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus angustifolius (narrow-leaved blue lupine)
Plasmid: PGEX-6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3)
References: UniProt: O04841, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
1323D 13C-separated NOESY
1422D doubly-tuned 13C 15N-filtered NOESY
15213C-edited 13C-filtered NOESY-HSQC
NMR detailsText: Determined using standard heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM U-15N, U-13C Ap4A hydrolase 1.6 mM ATP 20 mM U-100% 2H imidazole 32 mM NaF 20 mM MgCl290% H2O/10% D2O
21.6 mM U-15N, U-13C Ap4A hydrolase 1.6 mM ATP 20 mM U-100% 2H imidazole 32 mM NaF 20 mM MgCl2100% D2O
Sample conditionsIonic strength: 120 mM / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.2Variancollection
NMRPipe1.1Delaglio, et al.processing
XEASY1.4Bartels, et al.data analysis
DYANA1.5Guentert, et al.refinement
CNS1Brunger et al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2948 restraints. 2649 are NOE-based distance restraints, 299 are dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy, structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 30

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