BMRBj - BMREntryMaster

Found 1 Document (1.169 seconds)

BMRB: 4973

2K13

Sequential Assignment and Secondary Structure of Saratin, an Inhibitor of von Willebrand factor-dependent Platelet Adhesion to Collagen

Authors

Maurer, T., Bomke, J., Frech, M., Rysoik, T., Kalbitzer, H.R.

Assembly

Saratin

Entity

1. Saratin (polymer, Thiol state: all disulfide bound), 103 monomers, 12067.74 Da Detail

EEREDCWTFY ANRKYTDFDK SFKKSSDLDE CKKTCFKTEY CYIVFEDTVN KECYYNVVDG EELDQEKFVV DENFTENYLT DCEGKDAGNA AGTGDESDEV DED

Formula weight

12067.74 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS82:SG
2	disulfide	sing	1:CYS31:SG	1:CYS53:SG
3	disulfide	sing	1:CYS35:SG	1:CYS41:SG

Source organism

Hirudo medicinalis

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.9 %, Completeness (bb): 97.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.9 % (1129 of 1177)	98.2 % (598 of 609)	92.1 % (421 of 457)	99.1 % (110 of 111)
Backbone	97.7 % (604 of 618)	98.6 % (208 of 211)	96.7 % (294 of 304)	99.0 % (102 of 103)
Sidechain	94.8 % (623 of 657)	98.0 % (390 of 398)	89.6 % (225 of 251)	100.0 % (8 of 8)
Aromatic	82.6 % (114 of 138)	100.0 % (69 of 69)	64.7 % (44 of 68)	100.0 % (1 of 1)
Methyl	100.0 % (68 of 68)	100.0 % (34 of 34)	100.0 % (34 of 34)

1. saratin

EEREDCWTFY ANRKYTDFDK SFKKSSDLDE CKKTCFKTEY CYIVFEDTVN KECYYNVVDG EELDQEKFVV DENFTENYLT DCEGKDAGNA AGTGDESDEV DED

Show sample condition

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 2 Detail

Release date

2001-03-15

Citation 1

Sequential assignment and secondary structure of saratin, an inhibitor of von Willebrand factor-dependent platelet adhesion to collagen
Maurer, T., Bomke, J., Frech, M., Rysoik, T., Kalbitzer, H.R.
J. Biomol. NMR (2001), 21, 77-78, PubMed 11693575 , Abstract

Show more 1 citaion

Citation 2

No title is available
Neidig, K.

Hide non-primary 1 citaion

Related entities 1. Saratin, : 1 entities Detail

Experiments performed 7 experiments Detail

1 1H-15N NOESY

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

2 HNCA

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

3 HNCO

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

4 CBCA(CO)NH

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

5 HCCH-TOCSY

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

6 NOESY

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

7 TOCSY

Instrument

#1 Model Bruker DRX (800 MHz)

#2 Model Bruker DRX (500 MHz)

Sample #1

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	saratin			1.5 mM
2	H2O			100 %

Sample #2

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
3	saratin	[U-15N]		1.5 mM
4	H2O			100 %

Sample #3

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	saratin	[U-5% 13C; U-15N]		1.7 mM
6	H2O			100 %

Sample #4

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	saratin			1.5 mM
8	D2O			100 %

Sample #5

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
9	saratin	[U-15N]		1.5 mM
10	D2O			100 %

Sample #6

Temperature 298 (±2) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
11	saratin	[U-5% 13C; U-15N]		1.7 mM
12	D2O			100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4973_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:6:CYS:SG	1:82:CYS:SG	oxidized, CA 57.56, CB 46.83 ppm	oxidized, CA 54.82, CB 41.58 ppm	n/a
1:31:CYS:SG	1:53:CYS:SG	oxidized, CA 61.72, CB 45.63 ppm	oxidized, CA 52.5, CB 46.72 ppm	n/a
1:35:CYS:SG	1:41:CYS:SG	oxidized, CA 58.44, CB 39.62 ppm	oxidized, CA 59.26, CB 43.77 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr4973_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	set_1	Warning	1215		100.0 (chain: 1, length: 103)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: set_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 103, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
EEREDCWTFYANRKYTDFDKSFKKSSDLDECKKTCFKTEYCYIVFEDTVNKECYYNVVDGEELDQEKFVVDENFTENYLTDCEGKDAGNAAGTGDESDEV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EEREDCWTFYANRKYTDFDKSFKKSSDLDECKKTCFKTEYCYIVFEDTVNKECYYNVVDGEELDQEKFVVDENFTENYLTDCEGKDAGNAAGTGDESDEV

---
DED
|||
DED

Total number of assignments
- ¹³C chemical shifts: 436
- ¹H chemical shifts: 667
- ¹⁵N chemical shifts: 112

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	ARG	CZ	160.3
7	TRP	CD2	127.0
7	TRP	CE2	135.01
12	ASN	CG	179.06
13	ARG	CZ	160.55
17	ASP	CG	180.38
27	ASP	CG	180.24
29	ASP	CG	180.6
47	ASP	CG	180.06
50	ASN	CG	177.04
59	ASP	CG	179.43
65	GLN	CD	179.9
71	ASP	CG	179.56
73	ASN	CG	177.27
75	THR	HG1	6.11
77	ASN	CG	177.05
89	ASN	CG	178.53

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	457	420	91.9
¹H chemical shifts	609	598	98.2
¹⁵N chemical shifts	113	112	99.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	206	195	94.7
¹H chemical shifts	211	208	98.6
¹⁵N chemical shifts	103	102	99.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	251	225	89.6
¹H chemical shifts	398	390	98.0
¹⁵N chemical shifts	10	10	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	34	34	100.0
¹H chemical shifts	34	34	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	68	44	64.7
¹H chemical shifts	69	69	100.0
¹⁵N chemical shifts	1	1	100.0

Redox state of CYS
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: 1

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.169 seconds)

BMRB: 4973

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Saratin, : 1 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Instrument