BMRB Entry 18230

Name: Solution structure and dynamics of human S100A1 protein modified at cysteine 85 with homocysteine disulfide bond formation in calcium saturated form.
Published: 2013-02-18

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PDB ID: 2lp2
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18230
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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.

Deposition date:

2012-01-31

Original release date:

2013-02-18

Authors:

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

Citation:

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).
PubMed: 23351007

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET30a+

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
heteronucl_T1_relaxation
heteronucl_T2_relaxation

Data type	Count
13C chemical shifts	349
15N chemical shifts	95
1H chemical shifts	623
heteronuclear NOE values	231
T1 relaxation values	240
T2 relaxation values	240

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1
3	entity_2_1	2
4	entity_2_2	2
5	entity_2_3	2
6	entity_2_4	2
7	entity_3_1	3
8	entity_3_2	3

Entities:

Entity 1, entity_1_1 93 residues - 10414.62 Da.

Cysteine 85 is modified by disulfide bond formation with homocysteine

1

GLY

SER

GLU

LEU

GLU

THR

ALA

MET

GLU

THR

2

LEU

ILE

ASN

VAL

PHE

HIS

ALA

HIS

SER

GLY

3

LYS

GLU

GLY

ASP

LYS

TYR

LYS

LEU

SER

LYS

4

LYS

GLU

LEU

LYS

GLU

LEU

GLN

THR

GLU

5

LEU

SER

GLY

PHE

LEU

ASP

ALA

GLN

LYS

ASP

6

VAL

ASP

ALA

VAL

ASP

LYS

VAL

MET

LYS

GLU

7

LEU

ASP

GLU

ASN

GLY

ASP

GLY

GLU

VAL

ASP

8

PHE

GLN

GLU

TYR

VAL

LEU

VAL

ALA

9

LEU

THR

VAL

ALA

CYS

ASN

PHE

TRP

10

GLU

ASN

SER

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC (T1)	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (T1)	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (T1)	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (T2)	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (T2)	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC (T2)	sample_2	isotropic	sample_conditions_1
2D 15N-{1H} NOE	sample_2	isotropic	sample_conditions_1
2D 15N-{1H} NOE	sample_2	isotropic	sample_conditions_1
2D 15N-{1H} NOE	sample_2	isotropic	sample_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

BMRB	16360 17857 18087 18088 18089 18101 18231 18545
PDB	2JPT 2L0P 2LHL 2LLS 2LLT 2LLU 2LP2 2LP3 2LUX 2M3W
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
AlphaFold	P02639 P23297 Q5RC36