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- PDB-5t43: NMR Structure of Apo-form Human Tear Lipocalin -

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Basic information

Entry
Database: PDB / ID: 5t43
TitleNMR Structure of Apo-form Human Tear Lipocalin
ComponentsLipocalin-1
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


Transport of fatty acids / chloride ion binding / cysteine-type endopeptidase inhibitor activity / sensory perception of taste / signaling receptor binding / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
von Ebner's gland protein/ Bos/Can allergen / Lipocalin / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVogel, H.J. / Liu, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Alberta Innovates Health Solutions Canada
CitationJournal: To Be Published
Title: NMR Structure of Apo-form Human Tear Lipocalin
Authors: Vogel, H.J. / Liu, Z.
History
DepositionAug 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipocalin-1


Theoretical massNumber of molelcules
Total (without water)17,4541
Polymers17,4541
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 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lipocalin-1 / Tear lipocalin / Tlc / Tear prealbumin / TP / Von Ebner gland protein / VEG protein


Mass: 17453.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN1, VEGP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P31025
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D CBCA(CO)NH
141isotropic23D HN(CA)CB
151isotropic23D HNCO
161isotropic23D HN(CA)CO

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] Lipocalin, 90 % H2O, 10 % D2O, 50 mM sodium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O
Label: 15N/13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMLipocalin[U-99% 13C; U-99% 15N]1
90 %H2Onatural abundance1
10 %D2Onatural abundance1
50 mMsodium phosphatenatural abundance1
0.04 %sodium azidenatural abundance1
Sample conditionsDetails: 50 mM NaPi, pH 7.4 / Ionic strength: 50 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 20

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