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- PDB-2lp2: Solution structure and dynamics of human S100A1 protein modified ... -

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Basic information

Entry
Database: PDB / ID: 2lp2
TitleSolution structure and dynamics of human S100A1 protein modified at cysteine 85 with homocysteine disulfide bond formation in calcium saturated form
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN / Calcium bound form / EF-hand / calcium binding / helix reorientation / signaling protein / thionylation / small thiols
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
2-AMINO-4-MERCAPTO-BUTYRIC ACID / Protein S100-A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsNowakowski, M.E. / Jaremko, L. / Jaremko, M. / Zdanowski, K. / 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 2.2Oct 9, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,2828
Polymers20,8512
Non-polymers4316
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 / 198structures 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-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#3: Chemical
ChemComp-CA / CALCIUM ION


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

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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
1332D 1H-13C HSQC aliphatic
1432D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11133D (H)CCH-TOCSY
11233D 1H-13C NOESY aliphatic
11333D 1H-13C NOESY aromatic
11413D 1H-15N NOESY
11522D 1H-15N HSQC (T1)
11622D 1H-15N HSQC (T1)
11722D 1H-15N HSQC (T1)
11822D 1H-15N HSQC (T2)
11922D 1H-15N HSQC (T2)
12022D 1H-15N HSQC (T2)
12122D 15N-{1H} NOE
12222D 15N-{1H} NOE
12322D 15N-{1H} NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] S100A1 monomer, 10 mM Calcium ion, 50 mM TRIS-d11, 0.1 mM sodium azide, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] S100A1 monomer, 10 mM Calcium ion, 50 mM TRIS-d11, 0.1 mM sodium azide, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-98% 13C; U-98% 15N] S100A1 monomer, 10 mM Calcium ion, 50 mM TRIS-d11, 0.1 mM sodium azide, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMS100A1 monomer_1-1[U-98% 13C; U-98% 15N]1
10 mMCalcium ion-21
50 mMTRIS-d11-31
0.1 mMsodium azide-41
50 mMsodium chloride-51
1 mMS100A1 monomer_1-6[U-98% 15N]2
10 mMCalcium ion-72
50 mMTRIS-d11-82
0.1 mMsodium azide-92
50 mMsodium chloride-102
1 mMS100A1 monomer_1-11[U-98% 13C; U-98% 15N]3
10 mMCalcium ion-123
50 mMTRIS-d11-133
0.1 mMsodium azide-143
50 mMsodium chloride-153
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA4001
Varian UnityPlusVarianUNITYPLUS5002
Varian Uniform NMR SystemVarianUniform NMR System7003

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: standard sa.inp xplor NIH protocol
NMR constraintsNOE constraints total: 2800
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 198 / Conformers submitted total number: 20

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