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- PDB-2jyp: Coordinates for lowest energy structure of Aragonite protein-7, C... -

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Basic information

Entry
Database: PDB / ID: 2jyp
TitleCoordinates for lowest energy structure of Aragonite protein-7, C-terminal domain
ComponentsAragonite protein AP7
KeywordsUNKNOWN FUNCTION / Protein C-terminal fragment
Function / homologyshell calcification / protein homooligomerization / calcium ion binding / protein-containing complex / zinc ion binding / metal ion binding / Aragonite protein AP7
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model details36 AA C-terminal domain, AP7
Model type detailsminimized average
AuthorsCollino, S. / Kim, I. / Evans, J.
CitationJournal: Biochemistry / Year: 2008
Title: Identification and Structural Characterization of an Unusual RING-Like Sequence within an Extracellular Biomineralization Protein, AP7.
Authors: Collino, S. / Kim, I.W. / Evans, J.S.
History
DepositionDec 16, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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: Aragonite protein AP7


Theoretical massNumber of molelcules
Total (without water)4,3651
Polymers4,3651
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)1 / 1000structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Aragonite protein AP7


Mass: 4364.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q9BP37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 450 uM AP7C, 50 uM DTT, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
450 uMAP7C1
50 uMDTT1
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.chemical shift assignment
NMRPipeDelaglio, F. et al.processing
NMRPipeDelaglio, F. et al.data analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 1

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