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- PDB-2lb6: Structure of 18694Da MUP, typical to the major urinary protein fa... -

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Basic information

Entry
Database: PDB / ID: 2lb6
TitleStructure of 18694Da MUP, typical to the major urinary protein family: MUP9, MUP11, MUP15, MUP18 & MUP19
ComponentsMajor urinary protein 6
KeywordsTRANSPORT PROTEIN / lipocalin
Function / homology
Function and homology information


: / positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / cellular response to testosterone stimulus / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus ...: / positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / cellular response to testosterone stimulus / 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 / locomotor rhythm / negative regulation of lipid storage / small molecule binding / 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 6 / Major urinary protein 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsPhelan, M.M. / Mclean, L. / Beynon, R.J. / Hurst, J.L. / Lian, L.
Citation
Journal: To be Published
Title: Structural insights into the specificity of darcin, an atypical major urinary protein.
Authors: Phelan, M.M. / Mclean, L. / Beynon, R.J. / Hurst, J.L. / Lian, L.
#1: Journal: To be Published
Title: 1H, 15N and 13C resonance assignment of a common Major Urinary Protein of the mouse
Authors: Phelan, M.M. / Mclean, L. / Beynon, R.J. / Hurst, J.L. / Lian, L.
History
DepositionMar 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major urinary protein 6


Theoretical massNumber of molelcules
Total (without water)20,3671
Polymers20,3671
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 #1closest to the average

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Components

#1: Protein Major urinary protein 6 / MUP 6 / Alpha-2U-globulin / Group 1 / BS6


Mass: 20366.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57 / Gene: Mup6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02762, UniProt: P04938*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D HN(CA)CO
1813D HBHA(CO)NH
1913D HBHANH
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D 1H-15N NOESY
11412D CB(CGCD)HD aromatic
11513D (H)CCH-TOCSY aromatic

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] MUP11, 25 mM potassium phosphate, 0.2 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMUP11-1[U-98% 13C; U-98% 15N]1
25 mMpotassium phosphate-21
0.2 %sodium azide-31
Sample conditionsIonic strength: 25 / pH: 6.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1.3Bruker Biospincollection
TopSpin2.1.3Bruker Biospinprocessing
CcpNmr Analysis2.1.5CCPNMRdata analysis
CcpNmr Analysis2.1.5CCPNMRchemical shift assignment
CcpNmr Analysis2.1.5CCPNMRpeak picking
TALOSplusCornilescu, Delaglio and Baxdihedral angle determination
CYANA2.1 and 3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1 and 3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1 and 3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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