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- PDB-2lux: Calcium saturated form of human C85M S100A1 mutant -

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Basic information

Entry
Database: PDB / ID: 2lux
TitleCalcium saturated form of human C85M S100A1 mutant
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


RAGE receptor binding / 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 ...RAGE receptor binding / 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 / ER-Phagosome pathway / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsRuszczynska-Bartnik, K. / Budzinska, M. / Zdanowski, K. / Ejchart, A.
CitationJournal: To be Published
Title: Solution structure of human holo-S100A1 C85M mutant
Authors: Ruszczynska-Bartnik, K. / Ejchart, A. / Budzinska, M. / Zdanowski, K.
History
DepositionJun 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1May 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_ref_seq_dif / 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_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,0686
Polymers20,9072
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: 10453.641 Da / Num. of mol.: 2 / Mutation: C85M
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
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D 1H-15N NOESY
1523D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1713D CBCA(CO)NH
1813D HNCO
1913D HBHA(CO)NH
11013D HN(CO)CA
11132D 1H-15N HSQC edited for relaxation data

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] S100A1C85M, 50 mM [U-99% 2H] TRIS, 50 mM sodium chloride, 10 mM CALCIUM ION, 10 % [U-99% 2H] D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 13C; U-98% 15N] S100A1C85M, 50 mM [U-99% 2H] TRIS, 50 mM sodium chloride, 10 mM CALCIUM ION, 100 % [U-99% 2H] D2O, 100% D2O100% D2O
31 mM [U-99% 15N] S100A1C85M, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 10 mM CALCIUM ION, 10 % [U-99% 2H] D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMS100A1C85M-1[U-98% 13C; U-98% 15N]1
50 mMTRIS-2[U-99% 2H]1
50 mMsodium chloride-31
10 mMCALCIUM ION-41
10 %D2O-5[U-99% 2H]1
90 %H2O-61
1 mMS100A1C85M-7[U-98% 13C; U-98% 15N]2
50 mMTRIS-8[U-99% 2H]2
50 mMsodium chloride-92
10 mMCALCIUM ION-102
100 %D2O-11[U-99% 2H]2
1 mMS100A1C85M-12[U-99% 15N]3
50 mMTRIS-13[U-2H]3
50 mMsodium chloride-143
10 mMCALCIUM ION-153
10 %D2O-16[U-99% 2H]3
90 %H2O-173
Sample conditionsIonic strength: 0.05 / pH: 7.0 / Pressure: ambient / Temperature: 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

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardpeak picking
SparkyGoddarddata analysis
CARA1.8Keller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA3Peter Guntertchemical shift assignment
CYANA3Peter Guntertdata analysis
CYANA3Peter Guntertstructure solution
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry 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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