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- PDB-2lp3: Solution structure of S100A1 Ca2+ -

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Basic information

Entry
Database: PDB / ID: 2lp3
TitleSolution structure of S100A1 Ca2+
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN / calcium binding protein / S100 protein family
Function / homology
Function and homology information


Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of heart contraction / positive regulation of sprouting angiogenesis / substantia nigra development / positive regulation of nitric-oxide synthase activity / sarcoplasmic reticulum ...Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of heart contraction / positive regulation of sprouting angiogenesis / substantia nigra development / positive regulation of nitric-oxide synthase activity / sarcoplasmic reticulum / calcium-dependent protein binding / ATPase binding / ER-Phagosome pathway / intracellular signal transduction / calcium ion binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-A1 / 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 / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-A1 / 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 / 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 / simulated annealing
Model detailslowest energy, model 1
AuthorsBudzinska, M. / Ruszczynska-Bartnik, K. / Belczyk-Ciesielska, A. / Bierzynski, A. / Ejchart, A.
CitationJournal: Biochemistry / Year: 2013
Title: Impact of calcium binding and thionylation of S100A1 protein on its nuclear magnetic resonance-derived structure and backbone dynamics.
Authors: Nowakowski, M. / Ruszczynska-Bartnik, K. / Budzinska, M. / Jaremko, L. / Jaremko, M. / Zdanowski, K. / Bierzynski, A. / Ejchart, A.
History
DepositionJan 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A1
B: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0116
Polymers20,8512
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 210structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-A1 / S-100 protein alpha chain / S-100 protein subunit alpha / S100 calcium-binding protein A1


Mass: 10425.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A1, S100A / Production host: Escherichia coli (E. coli) / References: UniProt: P23297
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC NH2 only
2322D 1H-13C HSQC aliphatic
2422D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CO)CA
21123D 1H-13C NOESY aliphatic
21223D (H)CCH-TOCSY
21323D 1H-13C NOESY aromatic
11413D 1H-15N NOESY
11532D 1H-15N heteronuclear NOE
11632D 1H-15N heteronuclear NOE
11732D 1H-15N heteronuclear NOE
11832D 1H-15N T1 relaxation
11932D 1H-15N T1 relaxation
12032D 1H-15N T1 relaxation
12132D 1H-15N T2 relaxation
12232D 1H-15N T2 relaxation
12332D 1H-15N T2 relaxation

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Sample preparation

Details
Solution-IDContentsSolvent system
110 % D2O, 90 % H2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 13C; U-99% 15N] S100A1, 50 mM TRIS-d11, 90% H2O/10% D2O90% H2O/10% D2O
2100 % D2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 13C; U-99% 15N] S100A1, 50 mM TRIS-d11, 100% D2O100% D2O
310 % D2O, 90 % H2O, 50 mM sodium chloride, 10 mM CALCIUM ION, 0.8 mM [U-99% 15N] S100A1, 50 mM TRIS-d11, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 %D2O-11
90 %H2O-21
50 mMsodium chloride-31
10 mMCALCIUM ION-41
0.8 mMS100A1-5[U-99% 13C; U-99% 15N]1
50 mMTRIS-d11-61
100 %D2O-72
50 mMsodium chloride-82
10 mMCALCIUM ION-92
0.8 mMS100A1-10[U-99% 13C; U-99% 15N]2
50 mMTRIS-d11-112
10 %D2O-123
90 %H2O-133
50 mMsodium chloride-143
10 mMCALCIUM ION-153
0.8 mMS100A1-16[U-99% 15N]3
50 mMTRIS-d11-173
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1507.2ambient 310 K
2506.8ambient 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA4001
Varian UnityPlusVarianUNITYPLUS5002
Varian Varian NMR SystemVarianVarian NMR System7003
Varian Varian NMR SystemVarianVarian NMR System8004

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichconstraints assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 210 / Conformers submitted total number: 20

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