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- PDB-2lns: Solution structure of AGR2 residues 41-175 -

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Basic information

Entry
Database: PDB / ID: 2lns
TitleSolution structure of AGR2 residues 41-175
ComponentsAnterior gradient protein 2 homolog
KeywordsISOMERASE / Anterior-gradient Protein 2 / Thioredoxin-fold / cancer / adhesion / metastasis
Function / homology
Function and homology information


lung goblet cell differentiation / positive regulation of PERK-mediated unfolded protein response / mucus secretion / dystroglycan binding / positive regulation of developmental growth / positive regulation of cell-substrate adhesion / positive regulation of epidermal growth factor receptor signaling pathway / digestive tract morphogenesis / epidermal growth factor receptor binding / positive regulation of IRE1-mediated unfolded protein response ...lung goblet cell differentiation / positive regulation of PERK-mediated unfolded protein response / mucus secretion / dystroglycan binding / positive regulation of developmental growth / positive regulation of cell-substrate adhesion / positive regulation of epidermal growth factor receptor signaling pathway / digestive tract morphogenesis / epidermal growth factor receptor binding / positive regulation of IRE1-mediated unfolded protein response / positive regulation of protein localization to plasma membrane / inflammatory response / positive regulation of gene expression / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Thioredoxin-like / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Anterior gradient protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPatel, P. / Clarke, C.J. / Barraclough, D.L. / Rudland, P.S. / Barraclough, R. / Lian, L.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Metastasis-promoting anterior gradient 2 protein has a dimeric thioredoxin fold structure and a role in cell adhesion.
Authors: Patel, P. / Clarke, C. / Barraclough, D.L. / Jowitt, T.A. / Rudland, P.S. / Barraclough, R. / Lian, L.Y.
History
DepositionJan 4, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anterior gradient protein 2 homolog
B: Anterior gradient protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)32,3772
Polymers32,3772
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anterior gradient protein 2 homolog / AG-2 / hAG-2 / HPC8 / Secreted cement gland protein XAG-2 homolog


Mass: 16188.585 Da / Num. of mol.: 2 / Fragment: UNP residues 41-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGR2, AG2, UNQ515/PRO1030 / Production host: Escherichia coli (E. coli) / References: UniProt: O95994

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HN(COCA)CB
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1822D 1H-15N HSQC
1923D 1H-15N NOESY
11023D 1H-13C NOESY
1113IPAP
1124IPAP
11313D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] AGR2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N; Iled1-[13CH3]; Leu,Val-[13CH3]] AGR2, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-15N] AGR2, 10 mg Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-15N] AGR2, 5 % PEG:Hexanol, PEGPEG
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAGR2-1[U-13C; U-15N; U-2H]1
1 mMAGR2-2[U-13C; U-15N; U-2H]2
1 mMAGR2-3[U-15N]3
10 mg/mLPf1 phage-43
1 mMAGR2-5[U-15N]4
5 %PEG:Hexanol-64
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AnalysisCCPNpeak picking
AnalysisCCPNchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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