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- PDB-1nsh: Solution Structure of Rabbit apo-S100A11 (19 models) -

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Basic information

Entry
Database: PDB / ID: 1nsh
TitleSolution Structure of Rabbit apo-S100A11 (19 models)
ComponentsCalgizzarin
KeywordsMETAL BINDING PROTEIN / calcium-binding protein / EF hand / helix-loop-helix / S100 / Annexin
Function / homology
Function and homology information


S100 protein binding / calcium-dependent protein binding / regulation of cell population proliferation / calcium ion binding / extracellular space / nucleus / cytoplasm
Similarity search - Function
Protein S100-A11 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-A11 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
AuthorsDempsey, A.C. / Walsh, M.P. / Shaw, G.S.
CitationJournal: Structure / Year: 2003
Title: Unmasking the Annexin I Interaction from the structure of apo-S100A11
Authors: Dempsey, A.C. / Walsh, M.P. / Shaw, G.S.
History
DepositionJan 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calgizzarin
B: Calgizzarin


Theoretical massNumber of molelcules
Total (without water)22,6262
Polymers22,6262
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)19 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Calgizzarin / S100C protein


Mass: 11312.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: S100A11 OR S100C OR PCALG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P24480

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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 15N/13C-simultaneous NOESY
2323D 13C-edited/filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 13C,15N apo-S100A11, 50 mM KCl, 10 mM dithiothreitol, pH 7.2590% H2O, 10% D20
23 mM 13C,15N apo-S100A11, 3 mM unlabelled apo-S100A11, 50 mM KCl, 10 mM dithiothreitol, pH 7.25100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM KCl 7.25ambient 308 K
250 mM KCl 7.25ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
NMRPipe2.1F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, A. Baxprocessing
Pipp/Stapp4.3.3D. Garrett, G.M. Cloredata analysis
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using 2964 NOE derived distance restraints: 1336 intraresidue, 658 sequential, 594 short range, 264 long range and 112 intermonomer. There were 64 hydrogen bond ...Details: Structures were calculated using 2964 NOE derived distance restraints: 1336 intraresidue, 658 sequential, 594 short range, 264 long range and 112 intermonomer. There were 64 hydrogen bond distance restraints and 192 dihedral restraints included in calculations.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 19

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