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- PDB-2p3m: Solution structure of Mj0056 -

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Basic information

Entry
Database: PDB / ID: 2p3m
TitleSolution structure of Mj0056
ComponentsRiboflavin Kinase MJ0056
KeywordsTRANSFERASE / RIFT barrel / phosphotransferase / riboflavin kinase
Function / homology
Function and homology information


CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / nucleotide binding / magnesium ion binding
Similarity search - Function
Riboflavin kinase, archaeal / Riboflavin kinase domain, CTP-dependent / Riboflavin kinase, CTP-dependent / Domain of unknown function DUF120 / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsColes, M. / Truffault, V. / Djuranovic, S. / Martin, J. / Lupas, A.N.
CitationJournal: Structure / Year: 2007
Title: A CTP-Dependent Archaeal Riboflavin Kinase Forms a Bridge in the Evolution of Cradle-Loop Barrels.
Authors: Ammelburg, M. / Hartmann, M.D. / Djuranovic, S. / Alva, V. / Koretke, K.K. / Martin, J. / Sauer, G. / Truffault, V. / Zeth, K. / Lupas, A.N. / Coles, M.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: Riboflavin Kinase MJ0056


Theoretical massNumber of molelcules
Total (without water)15,7101
Polymers15,7101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Riboflavin Kinase MJ0056


Mass: 15709.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: Mj0056 / Plasmid: pET30b / Production host: Escherichia coli (E. coli)
References: UniProt: Q60365, CTP-dependent riboflavin kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
1313D NNH NOESY
141HNHA
151HNHB
1613D 13C-SEPARATED NOESY
1713D CNH NOESY
NMR detailsText: REPRESENTATIVE CONFORMER IS THE REGULARISED AVERAGE STRUCTURE

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Sample preparation

DetailsContents: 0.65 MM MJ0056 UNLABELLED MM PHOSPHATE BUFFER; 150 MM NAC 90% H2O,10% D2O; 0.65 MM MJ0056 U-15N; 30 MM PHOSPHATE BUFFER; 150 MM 90% H2O, 10% D2O; 0.65 MM MJ005 15N,13C; 30 MM PHOSPHATE BUFFER 150 MM NACL
Sample conditionsIonic strength: 150 mM / pH: 7.4 / Pressure: AMBIENT / Temperature: 300 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 DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.4BRUNGERrefinement
XwinNMR3.1structure solution
Sparkystructure solution
X-PLOR NIH2.9.4structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE SOLVED USING 839, DISTANCE RESTRAINTS, 56 HBOND RESTRAINTS, 399 DIHEDRAL RESTRAINTS AND 180 J-COUPLING RESTRAINTS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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