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- PDB-2go0: NMR solution structure of human pancreatitis-associated protein -

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Basic information

Entry
Database: PDB / ID: 2go0
TitleNMR solution structure of human pancreatitis-associated protein
ComponentsRegenerating islet-derived protein 3 alpha
KeywordsPROTEIN BINDING / C-type lectin / fibril
Function / homology
Function and homology information


disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides ...disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides / positive regulation of wound healing / acute-phase response / hormone activity / response to peptide hormone / response to wounding / negative regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / carbohydrate binding / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Regenerating islet-derived protein 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsChen, C.P. / Ho, M.R. / Lou, Y.C.
CitationJournal: To be Published
Title: Human pancreatitis-associated protein forms fibrillar aggregate with native-like conformation.
Authors: Ho, M.R. / Lou, Y.C. / Lin, W.C. / Lyu, P.C. / Chen, C.P.
History
DepositionApr 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: 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 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _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: Regenerating islet-derived protein 3 alpha


Theoretical massNumber of molelcules
Total (without water)15,1761
Polymers15,1761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
Representative

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Components

#1: Protein Regenerating islet-derived protein 3 alpha / Reg III-alpha / Pancreatitis-associated protein 1


Mass: 15175.892 Da / Num. of mol.: 1 / Fragment: residues 1-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06141

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM human pancreatitis-associated protein U-15N,13C; 20mM phosphate and 50mM NaCl buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM human pancreatitis-associated protein U-15N,13C; 20mM phosphate and 50mM NaCl buffer; 100% D2O100% D2O
Sample conditionspH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
NMRPipe5Delaglio, F.processing
AURELIA3.1.6Brukerdata analysis
X-PLOR2.9.4aSchwieters, C. D.structure solution
XwinNMR3.5Brukercollection
X-PLOR2.9.4arefinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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