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- PDB-2rps: Solution structure of a novel insect chemokine isolated from inte... -

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Basic information

Entry
Database: PDB / ID: 2rps
TitleSolution structure of a novel insect chemokine isolated from integument
ComponentsChemokine
KeywordsIMMUNE SYSTEM
Function / homologyChemokine
Function and homology information
Biological speciesPseudaletia separata (northern armyworm)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model type detailsminimized average
AuthorsKamiya, M. / Nakatogawa, S. / Oda, Y. / Kamijima, T. / Aizawa, T. / Demura, M. / Hayakawa, Y. / Kawano, K.
CitationJournal: Curr.Biol. / Year: 2009
Title: A novel peptide mediates aggregation and migration of hemocytes from an insect
Authors: Nakatogawa, S. / Oda, Y. / Kamiya, M. / Kamijima, T. / Aizawa, T. / Clark, K.D. / Demura, M. / Kawano, K. / Strand, M.R. / Hayakawa, Y.
History
DepositionJul 28, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemokine


Theoretical massNumber of molelcules
Total (without water)3,5451
Polymers3,5451
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 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Chemokine


Mass: 3545.007 Da / Num. of mol.: 1 / Fragment: UNP residues 21-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudaletia separata (northern armyworm)
Production host: Escherichia coli (E. coli) / References: UniProt: B7XBA7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D DQF-COSY
1412D 1H-1H NOESY
1523D 1H-15N NOESY
1623D 1H-15N TOCSY
1723D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11-3 mM protein, 0.010 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21-3 mM [U-15N] protein, 0.010 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity1
10 uMDSS1
1 mMentity[U-15N]2
10 uMDSS2
Sample conditionsIonic strength: 0 / pH: 5.1 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
JEOL ECAJEOLECA6002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ProcheckNMRLaskowski and MacArthurdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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