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- PDB-1df3: SOLUTION STRUCTURE OF A RECOMBINANT MOUSE MAJOR URINARY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1df3
TitleSOLUTION STRUCTURE OF A RECOMBINANT MOUSE MAJOR URINARY PROTEIN
ComponentsMAJOR URINARY PROTEIN
KeywordsTRANSPORT PROTEIN / LIPOCALIN / CARRIER PROTEIN / PHEROMONE / 8-STRANDED BETA-BARREL / BINDING POCKET / DISULFIDE BRIDGE (64-157) / SIGNALING PROTEIN
Function / homology
Function and homology information


pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...pheromone binding / positive regulation of lipid metabolic process / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / small molecule binding / locomotor rhythm / negative regulation of lipid storage / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Major urinary protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED ENERGY MINIMIZATION
AuthorsLuecke, C. / Franzoni, L. / Abbate, F. / Loehr, F. / Ferrari, E. / Sorbi, R.T. / Rueterjans, H. / Spisni, A.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: Solution structure of a recombinant mouse major urinary protein.
Authors: Lucke, C. / Franzoni, L. / Abbate, F. / Lohr, F. / Ferrari, E. / Sorbi, R.T. / Ruterjans, H. / Spisni, A.
#1: Journal: J.BIOMOL.NMR / Year: 1999
Title: Letter To the Editor: Complete 1H, 15N and 13C Assignment of a Recombinant Mouse Major Urinary Protein
Authors: Abbate, F. / Franzoni, L. / Loehr, F. / Luecke, C. / Ferrari, E. / Sorbi, R.T. / Rueterjans, H. / Spisni, A.
#2: Journal: FEBS Lett. / Year: 1997
Title: Expression of a Lipocalin in Pichia pastoris: Secretion, Purification and Binding Activity of a Recombinant Mouse Major Urinary Protein
Authors: Ferrari, E. / Lodi, T. / Sorbi, R.T. / Tirindelli, R. / Cavaggioni, A. / Spisni, A.
History
DepositionNov 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 / 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 1.4Nov 13, 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: MAJOR URINARY PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,7341
Polymers18,7341
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)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein MAJOR URINARY PROTEIN / MUP


Mass: 18733.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: LIVER / Production host: Pichia pastoris (fungus) / References: UniProt: P11589
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA, HN(CO)CA, HNCO, (HCA)CO(CA)NH, HCACO
121H(N)CA,CO, HN(CA)CB, HBHA(CC)(CO)NH, CC(CO)NH-TOCSY
131H(C)CH-TOCSY, (H)CB(CGC)CH-TOCSY, 3D 15N EDITED NOESY HSQC
1413D 13C EDITED NOESY HSQC, 1H 15N HSQC, 1H 13C HSQC
NMR detailsText: SPIN-SYSTEM HETEROGENEITIES DETECTED

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Sample preparation

DetailsContents: UNIFORMLY 15N- AND 13C/15N-LABELLED RECOMBINANT MUP FROM MOUSE; 10MM PHOSPHATE BUFFER
Sample conditionsIonic strength: 10mM PHOSPHATE / pH: 7.2 / Pressure: AMBIENT / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3BRUKERcollection
AURELIA2.5.9BRUKERdata analysis
DYANA1.5GUENTERTstructure solution
Discover97MSIrefinement
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED ENERGY MINIMIZATION / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2432 DISTANCE RESTRAINTS (481 INTRARESIDUAL, 580 SEQUENTIAL, 410 MEDIUM RANGE, 891 LONG RANGE AND 70 HYDROGEN BOND)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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