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- PDB-2iue: Pactolus I-domain: Functional Switching of the Rossmann Fold -

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Basic information

Entry
Database: PDB / ID: 2iue
TitlePactolus I-domain: Functional Switching of the Rossmann Fold
ComponentsINTEGRIN BETA-2-LIKE PROTEIN
KeywordsMEMBRANE PROTEIN / CD / ITC / LIMBS / MIDAS / ADMIDAS / MEMBRANE / INTEGRIN / TITRATION / CELL ADHESION / TRANSMEMBRANE
Function / homology
Function and homology information


integrin complex / cell adhesion mediated by integrin / cell-matrix adhesion / secretory granule / integrin-mediated signaling pathway / cell migration / integrin binding / signaling receptor activity / amyloid-beta binding / inflammatory response / focal adhesion
Similarity search - Function
Integrin beta-2 subunit / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. ...Integrin beta-2 subunit / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / von Willebrand factor, type A domain / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Integrin beta-2-like protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / DYANA AMBER 8.0, MODELLER8V2
AuthorsSen, M. / Legge, G.B.
CitationJournal: Proteins / Year: 2007
Title: Pactolus I-Domain: Functional Switching of the Rossmann Fold.
Authors: Sen, M. / Legge, G.B.
History
DepositionJun 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTEGRIN BETA-2-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,4341
Polymers23,4341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST POTENTIAL ENERGY ENSEMBLES
Representative

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Components

#1: Protein INTEGRIN BETA-2-LIKE PROTEIN / PROTEIN PACTOLUS SYNONYM: ADULT MALE BONE CDNA


Mass: 23433.660 Da / Num. of mol.: 1 / Fragment: PACTOLUS I-DOMAIN, RESIDUES 124-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3UV74
Sequence detailsTHE SEQUENCE IS DESCRIBED IN CHEN ET AL. J. BIOL. CHEM. 273 (15), 8711-8718 (1998)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HNCO
141HN(CA)CO
151HN(CA)CB
161CBCA(CO)NH
171HSQC- NOESY-HSQC
181CN-NOESY
191N- NOESY
1101N-TOCSY
NMR detailsText: STRUCTURES WERE INITIALLY CALCULATED BY DYANA, AND MODELLED BY THE MODELLER8V2,AND MINIMIZED BY THE AMBER8.0

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Sample preparation

DetailsContents: 5% D20, 10MM DTRIS (PH 6.9)
Sample conditionsIonic strength: 0 mM / pH: 6.9 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber8PONDER,J.W.refinement
NMRPipestructure solution
NMRViewstructure solution
DYANAstructure solution
Amber8structure solution
MOLMOLstructure solution
MODELLERstructure solution
RefinementMethod: DYANA AMBER 8.0, MODELLER8V2 / Software ordinal: 1
Details: AFTER CALCULATING THE STRUCTURES, ENSEMBLES WERE MODELLED BY PROGRAM MODELLER8V2
NMR ensembleConformer selection criteria: LOWEST POTENTIAL ENERGY ENSEMBLES
Conformers calculated total number: 200 / Conformers submitted total number: 20

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