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- PDB-1f3y: SOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE... -

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Basic information

Entry
Database: PDB / ID: 1f3y
TitleSOLUTION STRUCTURE OF THE NUDIX ENZYME DIADENOSINE TETRAPHOSPHATE HYDROLASE FROM LUPINUS ANGUSTIFOLIUS L.
ComponentsDIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE
KeywordsHYDROLASE / Enzyme / MIXED 4-STRANDED BETA SHEET / 2-STRANDED ANTIPARALLEL SHEET / ALPHA-BETA-ALPHA SANDWICH
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / chloroplast
Similarity search - Function
RNA pyrophosphohydrolase RppH / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...RNA pyrophosphohydrolase RppH / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Diadenosine 5',5'''-P1,P4-tetraphosphate hydrolase
Similarity search - Component
Biological speciesLupinus angustifolius (narrow-leaved blue lupine)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing
AuthorsSwarbrick, J.D. / Bashtannyk, T. / Maksel, D. / Zhang, X.R. / Blackburn, G.M. / Gayler, K.R. / Gooley, P.R.
CitationJournal: 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
DepositionJun 6, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 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


Theoretical massNumber of molelcules
Total (without water)18,8341
Polymers18,8341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with favorable non-bond energy,structures with the least restraint violations,target function
RepresentativeModel #3lowest energy

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Components

#1: Protein DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE HYDROLASE


Mass: 18834.172 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-199 / Mutation: Y1G/C2P/H3L/S4G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lupinus angustifolius (narrow-leaved blue lupine)
Plasmid: PGEX-6P-3 / Production host: Escherichia coli (E. coli)
References: UniProt: O04841, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCANH,CBCA(CO)NH,C(CO)NH TOCSY,HNCO,(HCA)CO(CA)NH
222HCACO,(H)CCH-TOCSY,13C-NOESY-HSQC,(HB)CB(CGCD)HD,(HB)CB(CGCDCE)HE,HACAHB,13C CT HEQC,
333HNHB,HNHA,15N-TOCSY-HSQC,15N-NOESY-HSQC,15N-IPAP-HSQC
44415N-NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9mM U-15N, 13C; Hydrolase 50mM phosphate buffer, 1.5mM EDTA, 3mM DTT90% H2O/10% D2O
20.9mM U-15N,13C; Hydrolase 50mM phosphate buffer, 1.3mM EDTA, 1.5mM EDTA,3mM DTT100% D2O
31.2mM U-15N; Hydrolase 50mM phosphate buffer, 1.5mM EDTA, 3mM DTT90% H2O/10% D2O
41.2mM U-15N; Hydrolase 20mM imidazole buffer, 20mM MGCl290% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM 6.5ambient 298 K
250mM 6.5ambient 298 K
350mM 6.5ambient 298 K
440mM 6.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Delaglioprocessing
XEASY1.3.13Bartelsdata analysis
DYANA1.5,1.4Guentertrefinement
CNS0.9Brungerrefinement
VNMR6.1 bVariancollection
RefinementMethod: torsion angle dynamics,simulated annealing / Software ordinal: 1
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: 25

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