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- PDB-2jyz: CG7054 solution structure -

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Basic information

Entry
Database: PDB / ID: 2jyz
TitleCG7054 solution structure
ComponentsCG7054-PA
KeywordsUNKNOWN FUNCTION / PEBP/RKIP / molecular modeling / chemical shift variations / titration / drosophila
Function / homology
Function and homology information


negative regulation of ERK1 and ERK2 cascade / cytosol
Similarity search - Function
Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsRautureau, G. / Jouvensal, L. / Vovelle, F. / Schoentgen, F. / Locker, D. / Decoville, M. / Damblon, C.
Citation
Journal: Proteins / Year: 2009
Title: NMR structure of a phosphatidyl-ethanolamine binding protein from Drosophila
Authors: Rautureau, G.J.P. / Vovelle, F. / Schoentgen, F. / Decoville, M. / Locker, D. / Damblon, C. / Jouvensal, L.
#1: Journal: J.Biomol.Nmr / Year: 2007
Title: 1H, 15N and 13C resonance assignments of CG7054, a new PEBP from Drosophila melanogaster
Authors: Rautureau, G. / Jouvensal, L. / Schoentgen, F. / Vovelle, F.
History
DepositionDec 21, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: 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_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 1.3May 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: CG7054-PA


Theoretical massNumber of molelcules
Total (without water)19,8431
Polymers19,8431
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)15 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein CG7054-PA / GH14779p / PEBP


Mass: 19843.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9VD02

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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-13C HSQC
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D HCACO
1823D HNHA
1913D HBHA(CO)NH
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D HN(CA)CB
11313D 1H-15N NOESY
11413D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM [U-13C; U-15N] Drosophila PEBP; 50mM potassium phosphate; 1mM DSS; 0.02% sodium azide; 90% H2O/10% D2O90% H2O/10% D2O
21.5mM [U-15N] Drosophila PEBP; 50mM potassium phosphate; 1mM DSS; 0.02% sodium azide; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMDrosophila PEBP[U-13C; U-15N]1
50 mMpotassium phosphate1
1 mMDSS1
0.02 %sodium azide1
1.5 mMDrosophila PEBP[U-15N]2
50 mMpotassium phosphate2
1 mMDSS2
0.02 %sodium azide2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ARIA2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1 / Details: CYANA, refinement in a water shell with ARIA
NMR constraintsNOE constraints total: 2787 / NOE long range total count: 999 / NOE medium range total count: 417 / NOE sequential total count: 1371 / Hydrogen bond constraints total count: 58 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 117 / Protein psi angle constraints total count: 117
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 15 / Maximum torsion angle constraint violation: 3.62 ° / Maximum upper distance constraint violation: 2.3 Å / Torsion angle constraint violation method: ARIA
NMR ensemble rmsDistance rms dev error: 0.26 Å

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