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BMRB Entry 18230

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18230
MolProbity Validation Chart

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Title: Solution structure and dynamics of human S100A1 protein modified at cysteine 85 with homocysteine disulfide bond formation in calcium saturated form.   PubMed: 23351007

Deposition date: 2012-01-31 Original release date: 2013-02-18

Authors: Nowakowski, Michal; Jaremko, Lukasz; Jaremko, Mariusz; Zdanowski, Konrad; Ejchart, Andrzej

Citation: Nowakowski, Micha; Ruszczyska-Bartnik, Katarzyna; Budziska, Monika; Jaremko, Lukasz; Jaremko, Mariusz; Zdanowski, Konrad; Bierzyski, Andrzej; Ejchart, Andrzej. "Impact of calcium binding and thionylation of S100A1 protein on its nuclear magnetic resonance-derived structure and backbone dynamics."  Biochemistry 52, 1149-1159 (2013).

Assembly members:
S100A1_monomer_1, polymer, 93 residues, 10414.62 Da.
CALCIUM ION, non-polymer, 40.078 Da.
2-AMINO-4-MERCAPTO-BUTYRIC ACID, non-polymer, 135.185 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
S100A1_monomer_1: GSELETAMETLINVFHAHSG KEGDKYKLSKKELKELLQTE LSGFLDAQKDVDAVDKVMKE LDENGDGEVDFQEYVVLVAA LTVACNNFFWENS

Data typeCount
13C chemical shifts349
15N chemical shifts95
1H chemical shifts623
heteronuclear NOE values231
T1 relaxation values240
T2 relaxation values240

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1_11
2entity_1_21
3entity_2_12
4entity_2_22
5entity_2_32
6entity_2_42
7entity_3_13
8entity_3_23

Entities:

Entity 1, entity_1_1 93 residues - 10414.62 Da.

Cysteine 85 is modified by disulfide bond formation with homocysteine

1   GLYSERGLULEUGLUTHRALAMETGLUTHR
2   LEUILEASNVALPHEHISALAHISSERGLY
3   LYSGLUGLYASPLYSTYRLYSLEUSERLYS
4   LYSGLULEULYSGLULEULEUGLNTHRGLU
5   LEUSERGLYPHELEUASPALAGLNLYSASP
6   VALASPALAVALASPLYSVALMETLYSGLU
7   LEUASPGLUASNGLYASPGLYGLUVALASP
8   PHEGLNGLUTYRVALVALLEUVALALAALA
9   LEUTHRVALALACYSASNASNPHEPHETRP
10   GLUASNSER

Entity 2, entity_2_1 - Ca - 40.078 Da.

1   CA

Entity 3, entity_3_1 - C4 H9 N O2 S - 135.185 Da.

1   HCS

Samples:

sample_1: S100A1 monomer_1, [U-98% 13C; U-98% 15N], 1 mM; Calcium ion 10 mM; TRIS-d11 50 mM; sodium azide 0.1 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_2: S100A1 monomer_1, [U-98% 15N], 1 mM; Calcium ion 10 mM; TRIS-d11 50 mM; sodium azide 0.1 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_3: S100A1 monomer_1, [U-98% 13C; U-98% 15N], 1 mM; Calcium ion 10 mM; TRIS-d11 50 mM; sodium azide 0.1 mM; sodium chloride 50 mM; D2O 100%

sample_conditions_1: pH: 7.2; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlysample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQC (T1)sample_2isotropicsample_conditions_1
2D 1H-15N HSQC (T1)sample_2isotropicsample_conditions_1
2D 1H-15N HSQC (T1)sample_2isotropicsample_conditions_1
2D 1H-15N HSQC (T2)sample_2isotropicsample_conditions_1
2D 1H-15N HSQC (T2)sample_2isotropicsample_conditions_1
2D 1H-15N HSQC (T2)sample_2isotropicsample_conditions_1
2D 15N-{1H} NOEsample_2isotropicsample_conditions_1
2D 15N-{1H} NOEsample_2isotropicsample_conditions_1
2D 15N-{1H} NOEsample_2isotropicsample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Varian INOVA 400 MHz
  • Varian UnityPlus 500 MHz
  • Varian Uniform NMR System 700 MHz

Related Database Links:

BMRB 16360 17857 18087 18088 18089 18101 18231 18545
PDB
DBJ BAE90380 BAG35086 BAG70130 BAG70260
EMBL CAA41107 CAH90674
GB AAH14392 AAI41992 AAI48020 AAP35584 AAP36328
PRF 2003367A
REF NP_001092512 NP_001127319 NP_001270255 NP_006262 XP_001111015
SP P02639 P23297 Q5RC36
TPG DAA31796

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts