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- PDB-2kax: Solution structure and dynamics of S100A5 in the apo and Ca2+ -bo... -

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Basic information

Entry
Database: PDB / ID: 2kax
TitleSolution structure and dynamics of S100A5 in the apo and Ca2+ -bound states
ComponentsProtein S100-A5
KeywordsMETAL BINDING PROTEIN / S100A5 / EF-hand / Calcium binding protein / Calcium / Polymorphism / Structural Genomics / SPINE2 / Structural Proteomics in Europe / SPINE / Structural Proteomics in Europe 2 / SPINE-2
Function / homology
Function and homology information


calcium-dependent protein binding / copper ion binding / neuronal cell body / calcium ion binding / protein homodimerization activity / zinc ion binding / nucleus
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 1, calcium-binding site ...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 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsBertini, I. / Das Gupta, S. / Hu, X. / Karavelas, T. / Luchinat, C. / Parigi, G. / Yuan, J. / Structural Proteomics in Europe (SPINE) / Structural Proteomics in Europe 2 (SPINE-2)
CitationJournal: J.Biol.Inorg.Chem. / Year: 2009
Title: Solution structure and dynamics of S100A5 in the apo and Ca2+-bound states
Authors: Bertini, I. / Das Gupta, S. / Hu, X. / Karavelas, T. / Luchinat, C. / Parigi, G. / Yuan, J.
History
DepositionNov 17, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: audit_author / pdbx_database_status ...audit_author / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_keywords.text
Revision 1.3Sep 16, 2020Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.4May 1, 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: Protein S100-A5
B: Protein S100-A5


Theoretical massNumber of molelcules
Total (without water)21,5192
Polymers21,5192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 350structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Protein S100-A5 / S100 calcium-binding protein A5 / Protein S-100D


Mass: 10759.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P33763

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2222D 1H-13C HSQC
2323D CBCA(CO)NH
2423D HNCO
2523D HNCA
2623D HN(CA)CB
2723D (H)CCH-TOCSY
2823D HBHA(CO)NH
1913D 1H-15N NOESY
21023D 1H-13C NOESY
11112D 1H-1H NOESY
11211H-15N NOE
113115N R1
114115N R2

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMprotein[U-100% 15N]1
0.4 mMprotein[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.5 ambient 298 K
20.1 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARA2Keller and Wuthrichchemical shift assignment
CARA2Keller and Wuthrichpeak picking
CARA2Keller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1562 / Protein phi angle constraints total count: 48 / Protein psi angle constraints total count: 48
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 350 / Conformers submitted total number: 31 / Representative conformer: 1

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