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- PDB-1ozo: Three-dimensional solution structure of apo-S100P protein determi... -

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Basic information

Entry
Database: PDB / ID: 1ozo
TitleThree-dimensional solution structure of apo-S100P protein determined by NMR spectroscopy
ComponentsS-100P protein
KeywordsMETAL BINDING PROTEIN / EF-hand / s100 protein
Function / homology
Function and homology information


RAGE receptor binding / S100 protein binding / microvillus membrane / transition metal ion binding / endothelial cell migration / : / sarcoplasmic reticulum / calcium-dependent protein binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction ...RAGE receptor binding / S100 protein binding / microvillus membrane / transition metal ion binding / endothelial cell migration / : / sarcoplasmic reticulum / calcium-dependent protein binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / cadherin binding / calcium ion binding / positive regulation of cell population proliferation / Neutrophil degranulation / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
S-100 / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. ...S-100 / 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 / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsLee, Y.-C. / Volk, D.E. / Thiviyanathan, V. / Kleerekoper, Q. / Gribenko, A.V. / Zhang, S. / Gorenstein, D.G. / Makhatadze, G.I. / Luxon, B.A.
CitationJournal: J.Biomol.Nmr / Year: 2004
Title: NMR structure of the Apo-S100P protein.
Authors: Lee, Y.-C. / Volk, D.E. / Thiviyanathan, V. / Kleerekoper, Q. / Gribenko, A.V. / Zhang, S. / Gorenstein, D.G. / Makhatadze, G.I. / Luxon, B.A.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: S-100P protein
B: S-100P protein


Theoretical massNumber of molelcules
Total (without water)20,7922
Polymers20,7922
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)16 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #15fewest violations,lowest energy

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Components

#1: Protein S-100P protein


Mass: 10395.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100P OR S100E / Production host: Escherichia coli (E. coli) / References: UniProt: P25815

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 2.5-3 mM S100P 15N/13C; 20 mM Tris-d6 buffer, 100mM KCl, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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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 UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIprocessing
Amber6/7David A. Case, David A. Pearlman, James W. Caldwell, Thomas E. Cheatham III, Junmei Wang, Wilson S.Ross, Carlos Simmerling, Tom Darden, Kenneth M. Merz, Robert V. Stanton, Ailan Cheng, James J.Vincent, Mike Crowley, Vickie Tsui, Holger Gohlke, Randall Radmer, Yong Duan, Jed Pitera, IrinaMassova, George L. Seibel, U. Chandra Singh, Paul Weiner, and Peter A. Kollmanstructure solution
DIAMDXu, Braunstructure solution
DIAMDXu, Braunrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3344 restraints, 3104 are NOE-derived distance constraints, 122 CSI-based torsional angle restraints
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 16

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