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- PDB-1jzu: Cell transformation by the myc oncogene activates expression of a... -

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Basic information

Entry
Database: PDB / ID: 1jzu
TitleCell transformation by the myc oncogene activates expression of a lipocalin: analysis of the gene (Q83) and solution structure of its protein product
Componentslipocalin Q83
KeywordsLIPID BINDING PROTEIN / BETA BARREL / LIPOCALIN
Function / homology
Function and homology information


oleic acid binding / enterobactin binding / arachidonate binding / defense response to bacterium / innate immune response / extracellular region
Similarity search - Function
Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Extracellular fatty acid-binding protein
Similarity search - Component
Biological speciesCoturnix coturnix (Common quail)
MethodSOLUTION NMR / ARIA, CNS automated refinement using also ambiguous NOE distance constraints; simulated annealing (torsion angle dynamics)
AuthorsHartl, M. / Matt, T. / Schueler, W. / Siemeister, G. / Kontaxis, G. / Kloiber, K. / Konrat, R. / Bister, K.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Cell Transformation by the v-myc Oncogene Abrogates c-Myc/Max-mediated Suppression of a C/EBPbeta-dependent Lipocalin Gene.
Authors: Hartl, M. / Matt, T. / Schueler, W. / Siemeister, G. / Kontaxis, G. / Kloiber, K. / Konrat, R. / Bister, K.
#1: Journal: J.Biomol.NMR / Year: 2000
Title: Sequence-Specific Resonance Assignments of Q83, a Lipocalin Highly Expressed in v-myc-Transformed Avian Fibroblasts
Authors: Kontaxis, G. / Matt, T. / Schueler, W. / Kraeutler, B. / Bister, K. / Konrat, R.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lipocalin Q83


Theoretical massNumber of molelcules
Total (without water)18,1051
Polymers18,1051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #15closest to the average

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Components

#1: Protein lipocalin Q83


Mass: 18104.734 Da / Num. of mol.: 1 / Mutation: A1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coturnix coturnix (Common quail) / Plasmid: pET3d-Q83 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9I9P7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D (H)CCH-TOCSY
1213D CCH-TOCSY-NNH
1313D NOESY-HSQC:(two 13C,Ca/methyl-centered,15N)
1413D HNHA
151Cross-correlated relaxation rates Ca(i)Ha(i)-DD/C'(i)-CSA
161Cross-correlated relaxation rates Ca(i)Ha(i)-DD/C'(i-1)-CSA

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Sample preparation

DetailsContents: 3mM lipocalin Q83 U-15N,13C; 20 mM potassium phosphate; 50 mM potassium chloride; 0.5mM dithiothreitol; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM potassium phosphate; 50mM potassium chloride; 0.5mM dithiothreitol
pH: 6.4 / Pressure: ambient / Temperature: 299 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 Rev BVarian Associates, Inc.collection
NMRPipe1.8 Rev 2001.030.21.27Delaglioprocessing
ANSIG3.3Kraulisdata analysis
NMRView4.1.3Johnson (Merck and Co., Inc.)data analysis
ARIA/CNS1Linge, Nilges, Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: ARIA, CNS automated refinement using also ambiguous NOE distance constraints; simulated annealing (torsion angle dynamics)
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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