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- PDB-2l5p: Solution NMR structure of protein lipocalin 12 from rat epididymis -

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Basic information

Entry
Database: PDB / ID: 2l5p
TitleSolution NMR structure of protein lipocalin 12 from rat epididymis
ComponentsLipocalin 12
KeywordsTRANSPORT PROTEIN / lipocalin / beta barrel
Function / homology
Function and homology information


Transport of fatty acids / retinoic acid binding / extracellular region
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Epididymal-specific lipocalin-12
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 5
AuthorsPeng, Y. / Lin, D.
CitationJournal: Proteins / Year: 2011
Title: Solution structure of the protein lipocalin 12 from rat epididymis
Authors: Peng, Y. / Zhang, X. / Liu, J. / Liu, Q. / Guo, C. / Zhang, Y. / Lin, D.
History
DepositionNov 3, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin 12


Theoretical massNumber of molelcules
Total (without water)21,3271
Polymers21,3271
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 / 320structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Lipocalin 12


Mass: 21327.189 Da / Num. of mol.: 1 / Fragment: residues 29-203 / Mutation: C176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lcn12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3EY83

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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
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1614D 1H-15N NOESY
1714D 1H-13C NOESY
1813D MQ-CCH-TOCSY
1913D HN(CO)CA
11013D HNCA

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Sample preparation

DetailsContents: 0.5mM [U-100% 13C; U-100% 15N] rLcn12-1, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: rLcn12-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20mM NaAC / pH: 4.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Advance III / Manufacturer: Bruker / Model: Advance III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.refinement
ARIA2.2Linge, O'Donoghue and Nilgeschemical shift assignment
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: 320 / Conformers submitted total number: 20 / Representative conformer: 5

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