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- PDB-2i3b: Solution Structure of a Human Cancer-Related Nucleoside Triphosphatase -

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Basic information

Entry
Database: PDB / ID: 2i3b
TitleSolution Structure of a Human Cancer-Related Nucleoside Triphosphatase
ComponentsHuman Cancer-Related NTPase
KeywordsHYDROLASE / NTPase / AAA / Rossmann
Function / homology
Function and homology information


CTPase activity / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / GTPase activity / ATP hydrolysis activity / RNA binding / ATP binding / membrane
Similarity search - Function
Nucleoside-triphosphatase, THEP1 type / NTPase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromosome 1 open reading frame 57, isoform CRA_d / Cancer-related nucleoside-triphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPlaczek, W.J. / Almeida, M.S. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: NMR Structure and Functional Characterization of a Human Cancer-related Nucleoside Triphosphatase.
Authors: Placzek, W.J. / Almeida, M.S. / Wuthrich, K.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: Human Cancer-Related NTPase


Theoretical massNumber of molelcules
Total (without water)20,6111
Polymers20,6111
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Human Cancer-Related NTPase / HCR-NTPase


Mass: 20610.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDRT1 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5TDE9, UniProt: Q9BSD7*PLUS, nucleoside-triphosphate phosphatase

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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-resolved aliphatic NOESY
1313D 13C-resolved aromatic NOESY

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Sample preparation

DetailsContents: 2 mM HCR-NTPase U-15N,13C; 25 mM MES buffer pH 6.4; 10 mM MgCl2; 5 mM DTT; 2 mM ATPgS; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 25mM MES, 10mM MgCl2 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
ATNOS/CANDIDversion 1.0Herrmann, T.data analysis
CYANAversion 1.0.3Guntert, P.structure solution
CYANAGuntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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