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- PDB-2lkt: Solution structure of N-terminal domain of human TIG3 in 2 M UREA -

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Basic information

Entry
Database: PDB / ID: 2lkt
TitleSolution structure of N-terminal domain of human TIG3 in 2 M UREA
ComponentsRetinoic acid receptor responder protein 3
KeywordsHYDROLASE / TIG3 / human tumor suppressor II family / NlpC/P60
Function / homology
Function and homology information


positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PE / N-acyltransferase activity / phospholipase A2 activity ...positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PE / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 / acyltransferase activity / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / negative regulation of cell population proliferation / membrane / cytoplasm / cytosol
Similarity search - Function
Lecithin retinol acyltransferase / LRAT domain profile. / LRAT domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phospholipase A and acyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, L. / Yu, W. / Xia, B.
CitationJournal: Biomol.Nmr Assign. / Year: 2012
Title: (1)H, (13)C, and (15)N resonance assignments of the N-terminal domain of human TIG3
Authors: Wang, L. / Yu, W. / Ren, X. / Lin, J. / Jin, C. / Xia, B.
History
DepositionOct 21, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor responder protein 3


Theoretical massNumber of molelcules
Total (without water)14,0511
Polymers14,0511
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 #1lowest energy

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Components

#1: Protein Retinoic acid receptor responder protein 3 / RAR-responsive protein TIG3 / Retinoid-inducible gene 1 protein / Tazarotene-induced gene 3 protein


Mass: 14050.886 Da / Num. of mol.: 1 / Fragment: NlpC/P60 structural domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIG3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UL19, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of N-terminal domain of human TIG3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY aliphatic
1413D 1H-13C NOESY aromatic
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HNCO
1913D HNCA
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] TIG3N protein-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 20 mM DTT-4, 2 M urea-5, 95 % H2O-6, 5 % [U-2H] D2O-7, 0.01 % DSS-8, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTIG3N protein-1[U-13C; U-15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
20 mMDTT-41
2 Murea-51
95 %H2O-61
5 %D2O-7[U-2H]1
0.01 %DSS-81
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
DYANA3Guntert, Braun and Wuthrichstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificpeak picking
ProcheckNMRLaskowski and MacArthurgeometry optimization
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
TopSpin3Bruker Biospincollection
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: using AMBER ff03 force filed refinement
NMR constraintsNOE constraints total: 3218 / NOE intraresidue total count: 1144 / NOE long range total count: 454 / NOE medium range total count: 233 / NOE sequential total count: 509
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.099 Å / Maximum upper distance constraint violation: 0.231 Å / Representative conformer: 1

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